Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor

Lost in translation: What we have learned from attributes that do not translate from Arabidopsis to other plants

Research in Arabidopsis thaliana has a powerful influence on our understanding of gene functions and pathways. However, not everything translates from Arabidopsis to crops and other plants. Here, a group of experts consider instances where translation has been lost and why such translation is not possible or is challenging. First, despite great efforts, floral dip transformation has not succeeded in other species outside Brassicaceae. Second, due to gene duplications and losses throughout evolution, it can be complex to establish which genes are orthologs of Arabidopsis genes. Third, during evolution Arabidopsis has lost arbuscular mycorrhizal symbiosis. Fourth, other plants have evolved specialized cell types that are not present in Arabidopsis. Fifth, similarly, C4 photosynthesis cannot be studied in Arabidopsis, which is a C3 plant. Sixth, many other plant species have larger genomes, which has given rise to innovations in transcriptional regulation that are not present in Arabidopsis. Seventh, phenotypes such as acclimation to water stress can be challenging to translate due to different measurement strategies. And eighth, while the circadian oscillator is conserved, there are important nuances in the roles of circadian regulators in crop plants. A key theme emerging across these vignettes is that even when translation is lost, insights can still be gained through comparison with Arabidopsis.

Transcriptomic profiling reveals bud dormancy stage dynamics in Japanese cedar (Cryptomeria japonica) throughout the nongrowing period

This study aimed to characterize the vegetative bud status of Japanese cedar (Cryptomeria japonica [L.f.] D. Don) throughout the nongrowing period (October-March). Based on the results of twig experiments and transcriptome analysis, we divided the nongrowing period into four stages. Buds were estimated to form between October and November (stage 1), with bud hardening continuing until December (stage 2). Endodormancy was released and transitioned into ecodormancy in mid-to-late December, with the timing varying by genotype. Buds endured harsh winter conditions during January and February (stage 3) and prepared for subsequent growth in March (stage 4). The number of days to bud burst (DBB) under forcing conditions gradually decreased after the transition to ecodormancy, culminating in bud burst in the field in late April. Transcriptome analysis identified key genes presumed to regulate these stages, such as CONSTANS-like and core clock genes. Furthermore, analysis of three genotypes with differing dormancy characteristics revealed DBB-associated genes, indicating the potential involvement of phytohormone cytokinins in regulating bud burst. Additionally, the PEBP- and SVP-like genes, known for their roles in dormancy regulation in other tree species, exhibited distinct expression patterns in Japanese cedar, highlighting variations in dormancy control mechanisms. This study is the first to categorize bud dormancy stages in conifers during the nongrowing period based on molecular data, and the results provide foundational insights for future investigations into conifer dormancy.

Effect of temperature on circadian clock functioning of trees in the context of global warming

Plant survival in a warmer world requires the timely adjustment of biological processes to cyclical changes in the new environment. Circadian oscillators have been proposed to contribute to thermal adaptation and plasticity. However, the influence of temperature on circadian clock performance and its impact on plant behaviour in natural ecosystems are not well-understood. We combined bioinformatics, molecular biology and ecophysiology to investigate the effects of increasing temperatures on the functioning of the circadian clock in two closely related tree species from Patagonian forests that constitute examples of adaptation to different thermal environments based on their altitudinal profiles. Nothofagus pumilio, the species from colder environments, showed a major rearrangement of its transcriptome and reduced ability to maintain rhythmicity at high temperatures compared with Nothofagus obliqua, which inhabits warmer zones. In altitude-swap experiments, N. pumilio, but not N. obliqua, showed limited oscillator function in warmer zones of the forest, and reduced survival and growth. Our findings show that interspecific differences in the influence of temperature on circadian clock performance are associated with preferred thermal niches, and to thermal plasticity of seedlings in natural environments, highlighting the potential role of a resonating oscillator in ecological adaptation to a warming environment.

MsLHY is an active regulator of cold resistance in alfalfa (Medicago sativa L.)

Low-temperature stress is a major environmental factor that limits the yield, quality, and geographical distribution of forage crops and restricts the development of the forage industry. As a core component of plant circadian clocks, Late Elongated Hypocotyl (LHY) plays a crucial role in regulating plant rhythms and responses to abiotic stress. However, the molecular mechanism by which LHY regulates the cold tolerance of alfalfa has not been reported. In this study, MsLHY, which is 2,235 bp in length and encodes 744 amino acids, was isolated from alfalfa. MsLHY was highly expressed in roots and stems and was significantly induced by low temperature. Transgenic MsLHY-overexpressing (OE) and RNAi alfalfa plants were obtained via Agrobacterium-mediated transformation. Under low-temperature stress, OE plants presented reduced reactive oxygen species accumulation and more osmotic regulatory substances, as well as greater antioxidant enzyme activity, to combat cold stress. Conversely, the RNAi plants presented trends opposite those of the OE plants. Furthermore, under cold stress, the overexpression of MsLHY upregulated the expression of the cold-responsive genes MsICE1, MsCBF1, MsCOR15A, and MsCML10, as well as the expression of the antioxidant-synthesizing genes MsSOD1 and MsCAT1, thereby increasing the cold tolerance of transgenic alfalfa. These results suggest that MsLHY plays an important role in increasing the cold tolerance of alfalfa.

Harmonizing time with survival: Circadian rhythm and autophagy in plants

BACKGROUND

Circadian rhythm (CR) is a self-sustaining biological oscillation that synchronizes physiological processes with the Earth's 24-h light-dark cycle. In plants, it regulates crucial physiological functions. Autophagy, a conserved degradation mechanism, maintains cellular homeostasis by recycling damaged organelles and proteins. Emerging evidence suggests an interplay between CRs and autophagy, optimizing plant survival and productivity.

SCOPE

This review explores the molecular mechanisms underlying CR and autophagy, highlighting their roles in growth and stress adaptation. It further examines how circadian clock components regulate autophagy-related genes (ATGs) in response to external cues.

MAJOR CONCLUSIONS

CR fine-tune autophagy by temporally regulating ATG gene expression. Key transcription factors, including TOC1 and LUX, modulate autophagic activity, ensuring energy conservation. Autophagy reciprocally influences circadian signaling, adjusting metabolic balance under stress.

GENERAL SIGNIFICANCE

Despite extensive research on circadian regulation, a comprehensive understanding of how core clock components orchestrate ATG gene expression remains lacking. Understanding the crosstalk between CR and autophagy provides insights into plant resilience and productivity, potentially informing crop improvement strategies that enhance stress tolerance and resource efficiency. This review aims to bridge this gap by summarizing recent insights and proposing future research directions.

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.

PHOTOPERIOD 1 enhances stress resistance and energy metabolism to promote spike fertility in barley under high ambient temperatures

High ambient temperature (HT) impairs reproductive development and grain yield in temperate crops. To ensure reproductive success under HT, plants must maintain developmental stability. However, the mechanisms integrating plant development and temperature resistance are largely unknown. Here, we demonstrate that PHOTOPERIOD 1 (PPD-H1), homologous to PSEUDO RESPONSE REGULATOR genes of the Arabidopsis (Arabidopsis thaliana) circadian clock, controls developmental stability in response to HT in barley (Hordeum vulgare). We analyzed the HT responses in independent introgression lines with either the ancestral wild-type Ppd-H1 allele or the natural ppd-h1 variant, selected in spring varieties to delay flowering and enhance yield under favorable conditions. HT delayed inflorescence development and reduced grain number in ppd-h1 mutant lines, while the wild-type Ppd-H1 genotypes exhibited accelerated reproductive development and showed a stable grain set under HT. CRISPR/Cas9-mediated genome editing of Ppd-H1 demonstrated that the CONSTANS, CO-like, and TOC1 domain of Ppd-H1 controls developmental stability, but not clock gene expression. Transcriptome and phytohormone analyses in developing leaves and inflorescences revealed increased expression levels of stress-responsive genes and abscisic acid levels in the leaf and inflorescence of the natural and induced mutant ppd-h1 lines. Furthermore, the ppd-h1 lines displayed downregulated photosynthesis- and energy metabolism-related genes, as well as decreased auxin and cytokinin levels in the inflorescence, which impaired anther and pollen development. In contrast, the transcriptome, phytohormone levels, and anther and pollen development remained stable under HT in the wild-type Ppd-H1 plants. Our findings suggest that Ppd-H1 enhances stress resistance and energy metabolism, thereby stabilizing reproductive development, floret fertility, and grain set under HT.

Genome-Wide Identification of the BREVIS RADIX Gene Family in Foxtail Millet: Function, Evolution, and Expression

BACKGROUND

Foxtail millet (Setaria italica), domesticated from green foxtail (Setaria viridis), is crucial for global food security. Given increasing environmental challenges, exploring its stress-resistance mechanisms via researching the BREVIS RADIX (BRX) gene family is urgent.

METHODS

The study combines advanced bioinformatics and experimental validation. It uses phylogenetic, motif, domain, synteny analyses, miRNA prediction, and quantitative expression profiling under stress.

RESULTS

Phylogenetic analysis reveals new sub-clades and trajectories. Motif and domain analyses find new conserved elements. Statistical models show unique selective forces. Synteny analysis identifies genomic architecture and new blocks. miRNA prediction reveals gene-miRNA interactions, and expression profiling shows new patterns.

CONCLUSIONS

The research offers new insights into the BRX family's role in foxtail millet's growth and stress responses, laying a foundation for crop genetic improvement and enhancing stress resilience for global food security.

Wake up: the regulation of dormancy release and bud break in perennial plants

In order to survive harsh winter conditions, perennial trees in the temperate and frigid regions enter a dormant state and cease growth in late summer after vigorous growth in spring and summer. After experiencing prolonged cold temperature and short days in winter, trees release their dormancy, and they resume growth to produce new buds in the following spring, a process known as bud break. The establishment/release of bud dormancy and bud break are crucial for the adaptations of woody plants and their survival in the natural environment. Photoperiod and temperature are key regulators in the bud dormancy and break cycle. In recent years, significant progress has been made in understanding the molecular mechanism for how photoperiod and temperature regulate seasonal growth and dormancy. Here, we summarized the regulatory network and mechanisms underlying the seasonal growth of perennial woody plants in the temperate and frigid regions, focusing on several molecular modules including the photoperiod, circadian clock, EARLY BUD BREAK 1 (EBB1) - SHORT VEGETATIVE PHASE Like (SVL) - EARLY BUD BREAK 3 (EBB3) module and hormone regulation. Through these modules, we will summarize how perennial trees release dormancy and bud break in order to better understand their differences and connections. By elucidating the interactions among these factors, we also point out the questions and challenges need to be addressed in understanding the bud dormancy and break cycle of perennial plants.

NTRC mediates the coupling of chloroplast redox rhythm with nuclear circadian clock in plant cells

The intricate interplay between cellular circadian rhythms, primarily manifested in the chloroplast redox oscillations-characterized by diel hyperoxidation/reduction cycles of 2-Cys peroxiredoxins-and the nuclear transcription/translation feedback loop (TTFL) machinery within plant cells, demonstrates a remarkable temporal coherence. However, the molecular mechanisms underlying the integration of these circadian rhythms remain elusive. In this study, we reveal that the chloroplast redox protein, NADPH-dependent thioredoxin reductase type C (NTRC), modulates the integration of the chloroplast redox rhythms and nuclear circadian clocks by regulating intracellular levels of reactive oxygen species and sucrose. In NTRC-deficient ntrc mutants, the perturbed temporal dynamics of cytosolic metabolite pools substantially attenuate the amplitude of CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) mRNA oscillation while maintaining its inherent periodicity. In contrast, these fluctuations extend the period and greatly reduced the amplitude of GIGANTEA (GI). In alignment with its regulatory role, the chloroplast redox rhythm and TTFL-driven nuclear oscillators are severely disrupted in ntrc plants. The impairements are rescued by NTRC expression but not by the expression of catalytically inactive NTRC(C/S) mutant, indicating that NTRC's redox activity is essential for synchronizing intracellular circadian rhythms. In return, the canonical nuclear clock component, TIMING OF CAB EXPRESSION 1 (TOC1), regulates the diel chloroplast redox rhythm by controlling NTRC expression, as evidenced by the redox cycle of chloroplast 2-Cys peroxiredoxins. This reciprocal regulation suggests a tight coupling between chloroplast redox rhythms and nuclear oscillators. Collectively, our study has identified NTRC as a key circadian modulator, elucidating the intricate connection between the metabolite-dependent chloroplast redox rhythm and the temporal dynamics of nuclear canonical clocks.

Translating weighted probabilistic bits to synthetic genetic circuits

Synthetic genetic circuits in plants could be the next technological horizon in plant breeding, showcasing potential for precise patterned control over expression. Nevertheless, uncertainty in metabolic environments prevents robust scaling of traditional genetic circuits for agricultural use, and studies show that a deterministic system is at odds with biological randomness. We analyze the necessary requirements for assuring Boolean logic gate sequences can function in unpredictable intracellular conditions, followed by interpreted pathways by which a mathematical representation of probabilistic circuits can be translated to biological implementation. This pathway is utilized through translation of a probabilistic circuit model presented by Pervaiz that works through a series of bits; each composed of a weighted matrix that reads inputs from the environment and a random number generator that takes the matrix as bias and outputs a positive or negative signal. The weighted matrix can be biologically represented as the regulatory elements that affect transcription near promotors, allowing for an electrical bit to biological bit translation that can be refined through tuning using invertible logic prediction of the input to output relationship of a genetic response. Failsafe mechanisms should be introduced, possibly through the use of self-eliminating CRISPR-Cas9, dosage compensation, or cybernetic modeling (where CRISPR is clustered regularly interspaced short palindromic repeats and Cas9 is clustered regularly interspaced short palindromic repeat-associated protein 9). These safety measures are needed for all biological circuits, and their implementation is needed alongside work with this specific model. With applied responses to external factors, these circuits could allow fine-tuning of organism adaptation to stress while providing a framework for faster complex expression design in the field.

EARLY FLOWERING 3 alleles affect the temperature responsiveness of the circadian clock in Chinese cabbage

Temperature is an environmental cue that entrains the circadian clock, adapting it to local thermal and photoperiodic conditions that characterize different geographic regions. Circadian clock thermal adaptation in leafy vegetables such as Chinese cabbage (Brassica rapa ssp. pekinensis) is poorly understood but essential to sustain and increase vegetable production under changing climates. We investigated circadian rhythmicity in natural Chinese cabbage accessions grown at 14, 20, and 28 °C. The circadian period was significantly shorter at 20 °C than at either 14 or 28 °C, and the responses to increasing temperature and temperature compensation (Q10) were associated with population structure. Genome-wide association studies mapping identified variation responsible for temperature compensation as measured by Q10 value for temperature increase from 20 to 28 °C. Haplotype analysis indicated that B. rapa EARLY FLOWERING 3 H1 Allele (BrELF3H1) conferred a significantly higher Q10 value at 20 to 28 °C than BrELF3H2. Co-segregation analyses of an F2 population derived from a BrELF3H1 × BrELF3H2 cross revealed that variation among BrELF3 alleles determined variation in the circadian period of Chinese cabbage at 20 °C. However, their differential impact on circadian oscillation was attenuated at 28 °C. Transgenic complementation in Arabidopsis thaliana elf3-8 mutants validated the involvement of BrELF3 in the circadian clock response to thermal cues, with BrELF3H1 conferring a higher Q10 value than BrELF3 H2 at 20 to 28 °C. Thus, BrELF3 is critical to the circadian clock response to ambient temperature in Chinese cabbage. These findings have clear implications for breeding new varieties with enhanced resilience to extreme temperatures.

Genome-wide identification and characterization of the bZIP family in the Mangrove Plant Kandelia obovata and its role in response to stress

BACKGROUND

The basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and responses to environmental changes. The mangrove plant Kandelia obovata, native to subtropical and tropical coastal intertidal zones, has evolved various adaptive mechanisms to cope with unstable muddy substrates, tidal fluctuations, saltwater intrusion, and intense ultraviolet radiation. This study aims to provide a comprehensive characterization of the bZIP gene family in K. obovata and investigate its functional roles in response to environmental stresses.

RESULTS

In the K. obovata genome, 66 bZIP genes were identified and named KobZIP1 to KobZIP66, categorized based on their chromosomal locations. These KobZIP genes exhibited diversity in physicochemical properties, such as protein length, molecular weight, and isoelectric point, and were all predicted to localize to the nucleus. Phylogenetic and structural analyses classified the KobZIP genes into 12 subfamilies, with subfamily A containing the majority of members. Gene structure analysis revealed variations in the number and position of exons and introns among subfamilies, reflecting their evolutionary history and potential functional diversity. Conserved motif analysis showed that all bZIP family members contained motifs in the basic and hinge regions, with subfamily D displaying the greatest motif diversity. Promoter region analysis identified various cis-acting elements associated with responses to phytohormones (ABA, GA, ET, IAA, MeJA, SA) and environmental stress. The expression patterns of KobZIP genes across different tissues and under various abiotic stress conditions were analyzed using transcriptomic data and experimental validation.

CONCLUSION

This study provides a comprehensive characterization and functional analysis of the bZIP gene family in K. obovata, offering new insights into their roles in plant development and environmental adaptation. The expression profiles of KobZIP genes during root development and post-embryonic stages, along with their responses to ABA, low temperature, and salt stress, underscore their potential significance in the adaptation of mangrove plants to the intertidal environment.

Maize inbreds show allelic variation for diel transcription patterns

Circadian entrainment and external cues can cause gene transcript abundance to oscillate throughout the day, and these patterns of diel transcript oscillation vary across genes and plant species. Less is known about within-species allelic variation for diel patterns of transcript oscillation, or about how regulatory sequence variation influences diel transcription patterns. In this study, we evaluated diel transcript abundance for 24 diverse maize inbred lines. We observed extensive natural variation in diel transcription patterns, with two-fold variation in the number of genes that oscillate over the course of the day. A convolutional neural network trained to predict oscillation from promoter sequence identified sequences previously reported as binding motifs for known circadian clock genes in other plant systems. Genes showing diel transcription patterns that cosegregate with promoter sequence haplotypes are enriched for associations with photoperiod sensitivity and may have been indirect targets of selection as maize was adapted to longer day lengths at higher latitudes. These findings support the idea that cis-regulatory sequence variation influences patterns of gene expression, which in turn can have effects on phenotypic plasticity and local adaptation.

The clock-associated LUX ARRHYTHMO regulates high-affinity nitrate transport in Arabidopsis roots

The circadian clock organizes physiological processes in plants to occur at specific times of the day, optimizing efficient use of resources. Nitrate is a crucial inorganic nitrogen source for agricultural systems to sustain crop productivity. However, because nitrate fertilization has a negative impact on the environment, it is important to carefully manage nitrate levels. Understanding crop biological rhythms can lead to more ecologically friendly agricultural practices. Gating responses through the circadian clock could be a strategy to enhance root nitrate uptake and to limit nitrate runoff. In Arabidopsis, the NITRATE TRANSPORTER 2.1 (NRT2.1) gene encodes a key component of the high-affinity nitrate transporter system. Our study reveals that NRT2.1 exhibits a rhythmic expression pattern, with daytime increases and nighttime decreases. The NRT2.1 promoter activity remains rhythmic under constant light, indicating a circadian regulation. The clock-associated transcription factor LUX ARRHYTHMO (LUX) binds to the NRT2.1 promoter in vivo. Loss-of-function of LUX leads to increased NRT2.1 transcript levels and root nitrate uptake at dusk. This supports LUX acting as a transcriptional repressor and modulating NRT2.1 expression in a time-dependent manner. Furthermore, applying nitrate at different times of the day results in varying magnitudes of the transcriptional response in nitrate-regulated genes. We also demonstrate that a defect in the high-affinity nitrate transport system feeds back to the central oscillator by modifying the LUX promoter activity. In conclusion, this study uncovers a molecular pathway connecting the root nitrate uptake and circadian clock, with potential agro-chronobiological applications.

Integrated eQTL mapping approach reveals genomic regions regulating candidate genes of the E8-r3 locus in soybean

Deciphering the gene regulatory networks of critical quantitative trait loci associated with early maturity provides information for breeders to unlock soybean's (Glycine max (L.) Merr.) northern potential and expand its cultivation range. The E8-r3 locus is a genomic region regulating the number of days to maturity under constant short-day photoperiodic conditions in two early-maturing soybean populations (QS15524F2:F3 and QS15544RIL) belonging to maturity groups MG00 and MG000. In this study, we developed a combinatorial expression quantitative trait loci mapping approach using three algorithms (ICIM, IM, and GCIM) to identify the regions that regulate three candidate genes of the E8-r3 locus (Glyma.04G167900/GmLHCA4a, Glyma.04G166300/GmPRR1a, and Glyma.04G159300/GmMDE04). Using this approach, a total of 2,218 trans (2,061 genes)/7 cis (7 genes) and 4,073 trans (2,842 genes)/3,083 cis (2,418 genes) interactions were mapped in the QS15524F2:F3 and QS15544RIL populations, respectively. From these interactions, we successfully identified two hotspots (F2_GM15:49,385,092-49,442,237 and F2_GM18:1,434,182-1,935,386) and three minor regions (RIL_GM04:17,227,512-20,251,662, RIL_GM04:31,408,946-31,525,671 and RIL_GM13:37,289,785-38,620,690) regulating the candidate genes of E8-r3 and several of their homologs. Based on co-expression network and single nucleotide variant analyses, we identified ALTERED PHLOEM DEVELOPMENT (Glyma.15G263700) and DOMAIN-CONTAINING PROTEIN 21 (Glyma.18G025600) as the best candidates for the F2_GM15:49,385,092-49,442,237 and F2_GM18:1,434,182-1,935,386 hotspots. These findings demonstrate that a few key regions are involved in the regulation of the E8-r3 candidates GmLHCA4a, GmPRR1a, and GmMDE04.

Transcriptome Analysis Reveals Genes Responsive to Three Low-Temperature Treatments in Arabidopsis thaliana

Cold stress impedes the growth and development of plants, restricts the geographical distribution of plant species, and impacts crop productivity. In this study, we analyzed the Arabidopsis thaliana transcriptome to identify differentially expressed genes (DEGs) in 14-day-old plantlets exposed to temperatures of 0 °C, 4 °C, and 10 °C for 24 h, compared to the 22 °C control group. Among the top 50 cold-induced genes at each temperature, we identified 31 genes that were common across all three low temperatures, with nine genes common to 0-4 °C, eight genes to 4-10 °C, and two genes to 0-10 °C. Using q-RTPCR, we analyzed selected genes at 24, 48, and 72 h under the three low temperatures. Our data revealed that genes, such as galactinol synthase 3 (Gols3, At1g09350), CIR1 (At5g37260), DnaJ (At1g71000), and At5g05220 (unknown function), exhibited the highest expressions at 0 °C and 4 °C throughout all time points. We also studied genes from the UDP-glycosyltransferase (UGT78) family, including At5g17030 (D3), At5g17040 (D4), At5g17050 (D2), and At1g30530 (D1), which showed increased expression at low temperatures compared to plantlets at 22 °C for 24 h. Gene ontology analysis revealed that DEGs highly enriched were found in biological processes such as "RNA secondary structure unwinding" and "rRNA processing" induced at the three low temperatures, whereas processes related to photosynthesis were repressed. Our findings indicated upregulation in the expression of four RNA helicases (RH13, RH48, RH32, and RH29), belonging to the "RNA secondary structure unwinding" category, mainly at 0 °C and 4 °C. This study provides valuable information on the molecular mechanisms that activate Arabidopsis thaliana in its early response to these three low temperatures.

Genome-Wide Identification and Expression Profiling Analysis of the CCT Gene Family in Solanum lycopersicum and Solanum melongena

CCT family genes play crucial roles in photoperiodic flowering and environmental stress response; however, there are limited reports in Solanum species with considerable edible and medicinal value. In this study, we conducted genome-wide characterization and expression profiling analysis of the CCT gene family in two Solanum species: tomato (Solanum lycopersicum L.) and eggplant (Solanum melongena L.). A total of 27 SlCCT and 29 SmCCT genes were identified in the tomato and eggplant genomes, respectively. Phylogenetic analysis showed that the CCT gene family could be divided into six subgroups (COL I, COL II, COL III, PRR, CMF I, and CMF II) in Oryza sativa and Arabidopsis thaliana. The similarity in the distribution of exon-intron structures and conserved motifs within the same subgroup indicated the conservation of SlCCT and SmCCT genes during evolution. Intraspecies collinearity analysis revealed that six pairs of SlCCT genes and seven pairs of SmCCT genes showed collinear relationships, suggesting that segmental duplication played a vital role in the expansion of the SlCCT and SmCCT family genes. Cis-acting element prediction indicated that SlCCT and SmCCT were likely to be involved in multiple responses stimulated by light, phytohormones, and abiotic stress. RT-qPCR analysis revealed that SmCCT15, SlCCT6/SlCCT14, and SlCCT23/SmCCT9 responded significantly to salt, drought, and cold stress, respectively. Our comprehensive analysis of the CCT gene family in tomato and eggplant provides a basis for further studies on its molecular role in regulating flowering and resistance to abiotic stress, and provides valuable candidate gene resources for tomato and eggplant molecular breeding.

The overexpression of the switchgrass (Panicum virgatum L.) genes PvTOC1-N or PvLHY-K affects circadian rhythm and hormone metabolism in transgenic Arabidopsis seedlings

Switchgrass (Panicum virgatum L.) is a perennial C4 warm-season grass known for its high-biomass yield and wide environmental adaptability, making it an ideal bioenergy crop. Despite its potential, switchgrass seedlings grow slowly, often losing out to weeds in field conditions and producing limited biomass in the first year of planting. Furthermore, during the reproductive growth stage, the above-ground biomass rapidly increases in lignin content, creating a significant saccharification barrier. Previous studies have identified rhythm-related genes TOC1 and LHY as crucial to the slow seedling development in switchgrass, yet the precise regulatory functions of these genes remain largely unexplored. In this study, the genes TOC1 and LHY were characterized within the tetraploid genome of switchgrass. Gene expression analysis revealed that PvTOC1 and PvLHY exhibit circadian patterns under normal growth conditions, with opposing expression levels over time. PvTOC1 genes were predominantly expressed in florets, vascular bundles, and seeds, while PvLHY genes showed higher expression in stems, leaf sheaths, and nodes. Overexpression of PvTOC1 from the N chromosome group (PvTOC1-N) or PvLHY from the K chromosome group (PvLHY-K) in Arabidopsis thaliana led to alterations in circadian rhythm and hormone metabolism, resulting in shorter roots, delayed flowering, and decreased resistance to oxidative stress. These transgenic lines exhibited reduced sensitivity to hormones and hormone inhibitors, and displayed altered gene expression in the biosynthesis and signal transduction pathways of abscisic acid (ABA), gibberellin (GA), 3-indoleacetic acid (IAA), and strigolactone (SL). These findings highlight roles of PvTOC1-N and PvLHY-K in plant development and offer a theoretical foundation for genetic improvements in switchgrass and other crops.

Interaction between plant-specific transcription factors TCP and YABBY expressed in the tendrils of the melon Cucumis melo

Plant tendrils are specialized organs that can twine around other structures to facilitate climbing. They occur in a variety of plant families and have diverse ontogenic origins. In cucurbits, tendrils originate from lateral shoots. Fine mapping verified that the tendril-less ctl mutation of the melon Cucumis melo corresponds to a frameshift mutation in the CmTCP1 gene, which encodes a TCP transcription factor. A yeast two-hybrid screen for CmTCP1/CTL-interacting proteins identified a member of the plant-specific YABBY transcription factor family, which was named CmYAB1. Each of the N- and C-terminal regions of CmTCP1 interacted with CmYAB1. The ctl mutation impaired the interaction between CmTCP1 and CmYAB1. Both proteins interacted in vitro and were localized to the nucleus in plant cells. In situ expression analysis revealed the coexistence of the CmTCP1 and CmYAB1 mRNAs in the abaxial domains of developing tendrils. An RNA-seq analysis of the seven YABBY genes in the melon genome revealed relatively high expression ratios of CmYAB1 in tendrils compared with those in leaves. These results suggest a novel function of the YABBY protein through its interaction with a TCP protein in the development of cucurbit tendrils.

The PRR-EC complex and SWR1 chromatin remodeling complex function cooperatively to repress nighttime hypocotyl elongation by modulating PIF4 expression in Arabidopsis

The circadian clock entrained by environmental light-dark cycles enables plants to fine-tune diurnal growth and developmental responses. Here, we show that physical interactions among evening clock components, including PSEUDO-RESPONSE REGULATOR 5 (PRR5), TIMING OF CAB EXPRESSION 1 (TOC1), and the Evening Complex (EC) component EARLY FLOWERING 3 (ELF3), define a diurnal repressive chromatin structure specifically at the PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) locus in Arabidopsis. These three clock components act interdependently as well as independently to repress nighttime hypocotyl elongation, as hypocotyl elongation rate dramatically increased specifically at nighttime in the prr5-1 toc1-21 elf3-1 mutant, concomitantly with a substantial increase in PIF4 expression. Transcriptional repression of PIF4 by ELF3, PRR5, and TOC1 is mediated by the SWI2/SNF2-RELATED (SWR1) chromatin remodeling complex, which incorporates histone H2A.Z at the PIF4 locus, facilitating robust epigenetic suppression of PIF4 during the evening. Overall, these findings demonstrate that the PRR-EC-SWR1 complex represses hypocotyl elongation at night through a distinctive chromatin domain covering PIF4 chromatin.

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.

CIRCADIAN CLOCK-ASSOCIATED1 Delays Flowering by Directly Inhibiting the Transcription of BcSOC1 in Pak-choi

Flowering is critical to the success of plant propagation. The MYB family transcription factor CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) is an essential component of the core loop of the circadian clock and plays a crucial role in regulating plant flowering time. In this study, we found that photoperiod affects the expression pattern and expression level of BcCCA1, which is delayed flowering time under short-day conditions in Pak-choi [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. We detected overexpression and silencing of BcCCA1 in Pak-choi, resulting in delayed and promoted flowering time, respectively. Furthermore, we also discovered that FLOWERING LOCUS C (BcFLC) and SUPPRESSOR OF CONSTANS1 (BcSOC1) were expressed significantly differently in BcCCA1 overexpression and silencing plants compared with control plants. Therefore, we further investigated the interaction relationship between BcCCA1, BcFLC, and BcSOC1, and the results showed that BcCCA1 and BcFLC as a complex interacted with each other. Moreover, both BcCCA1 and BcFLC can directly bind to the promoter of BcSOC1 and repress its transcription, and BcCCA1 can form a complex with BcFLC to enhance the transcriptional inhibition of BcSOC1 by BcFLC. This study reveals a new mechanism by which the circadian clock regulates flowering time.

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.

Unlocking Nature's Rhythms: Insights into Secondary Metabolite Modulation by the Circadian Clock

Plants, like many other living organisms, have an internal timekeeper, the circadian clock, which allows them to anticipate photoperiod rhythms and environmental stimuli to optimally adjust plant growth, development, and fitness. These fine-tuned processes depend on the interaction between environmental signals and the internal interactive metabolic network regulated by the circadian clock. Although primary metabolites have received significant attention, the impact of the circadian clock on secondary metabolites remains less explored. Transcriptome analyses revealed that many genes involved in secondary metabolite biosynthesis exhibit diurnal expression patterns, potentially enhancing stress tolerance. Understanding the interaction mechanisms between the circadian clock and secondary metabolites, including plant defense mechanisms against stress, may facilitate the development of stress-resilient crops and enhance targeted management practices that integrate circadian agricultural strategies, particularly in the face of climate change. In this review, we will delve into the molecular mechanisms underlying circadian rhythms of phenolic compounds, terpenoids, and N-containing compounds.

Arabidopsis seeds altered in the circadian clock protein TOC1 are characterized by higher level of linolenic acid

The circadian clock plays a critical role in regulating plant physiology and metabolism. However, the way in which the clock impacts the regulation of lipid biosynthesis in seeds is partially understood. In the present study, we characterized the seed fatty acid (FA) and glycerolipid (GL) compositions of pseudo-response regulator mutants. Among these mutants, toc1 (timing of cab expression 1) exhibited the most significant differences compared to control plants. These included an increase in total FA content, characterized by elevated levels of linolenic acid (18:3) along with a reduction in linoleic acid (18:2). Furthermore, our findings revealed that toc1 developing seeds showed increased expression of genes related to FA metabolism. Our results show a connection between TOC1 and lipid metabolism in Arabidopsis seeds.

Genome-scale identification, expression and evolution analysis of B-box members in Dendrobium huoshanense

B-box (BBX) proteins have been recognized as vital determinants in plant development, morphogenesis, and adaptive responses to a myriad of environmental stresses. These zinc-finger proteins play a pivotal role in various biological processes. Their influence spans photomorphogenesis, the regulation of flowering, and imparting resilience to a wide array of challenges, encompassing both biotic and abiotic factors. Chromosome localization, gene structure and conserved motifs, phylogenetic analysis, collinearity analysis, expression profiling, fluorescence quantitative analysis, and tobacco transient transformation methods were used for functional localization and expression pattern analysis of the DhBBX gene. A total of 23 DhBBX members were identified from Dendrobium huoshanense. Subsequent phylogenetic evaluations effectively segregated these genes into five discrete evolutionary subsets. The predictions of subcellular localizations revealed that all these proteins were localized in the nucleus. The genetic composition and patterns showed that the majority of these genes consisted of several exons, with a few variations that could be attributed to transposon insertion. A comprehensive analysis using qRT-PCR was conducted to unravel the expression patterns of these genes in D. huoshanense, with a specific concentration on their responses to various hormone treatments and cold stress. Subcellular localization reveals that DhBBX21 and DhBBX9 are located in the nucleus. Our results provide a deep comprehension of the complex regulatory mechanisms of BBXs in response to various environmental and hormonal stimuli. These discoveries encourage further detailed and focused investigations into the operational dynamics of the BBX gene family in a wider range of plant species.

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.

OsCOL5 suppresses heading through modulation of Ghd7 and Ehd2, enhancing rice yield

KEY MESSAGE

OsCOL5, an ortholog of Arabidopsis COL5, is involved in photoperiodic flowering and enhances rice yield through modulation of Ghd7 and Ehd2 and interactions with OsELF3-1 and OsELF3-2. Heading date, also known as flowering time, plays a crucial role in determining the adaptability and yield potential of rice (Oryza sativa L.). CONSTANS (CO)-like is one of the most critical flowering-associated gene families, members of which are evolutionarily conserved. Here, we report the molecular functional characterization of OsCOL5, an ortholog of Arabidopsis COL5, which is involved in photoperiodic flowering and influences rice yield. Structural analysis revealed that OsCOL5 is a typical member of CO-like family, containing two B-box domains and one CCT domain. Rice plants overexpressing OsCOL5 showed delayed heading and increases in plant height, main spike number, total grain number per plant, and yield per plant under both long-day (LD) and short-day (SD) conditions. Gene expression analysis indicated that OsCOL5 was primarily expressed in the leaves and stems with a diurnal rhythm expression pattern. RT-qPCR analysis of heading date genes showed that OsCOL5 suppressed flowering by up-regulating Ghd7 and down-regulating Ehd2, consequently reducing the expression of Ehd1, Hd3a, RFT1, OsMADS14, and OsMADS15. Yeast two-hybrid experiments showed direct interactions of OsCOL5 with OsELF3-1 and OsELF3-2. Further verification showed specific interactions between the zinc finger/B-box domain of OsCOL5 and the middle region of OsELF3-1 and OsELF3-2. Yeast one-hybrid assays revealed that OsCOL5 may bind to the CCACA motif. The results suggest that OsCOL5 functions as a floral repressor, playing a vital role in rice's photoperiodic flowering regulation. This gene shows potential in breeding programs aimed at improving rice yield by influencing the timing of flowering, which directly impacts crop productivity.

Genome-wide identification, molecular evolution and expression analysis of the B-box gene family in mung bean (Vigna radiata L.)

BACKGROUND

Mung bean (Vigna radiata L.) is an important warm-season grain legume. Adaptation to extreme environmental conditions, supported by evolution, makes mung bean a rich gene pool for stress tolerance traits. The exploration of resistance genes will provide important genetic resources and a theoretical basis for strengthening mung bean breeding. B-box (BBX) proteins play a major role in developmental processes and stress responses. However, the identification and analysis of the mung bean BBX gene family are still lacking.

RESULTS

In this study, 23 VrBBX genes were identified through comprehensive bioinformatics analysis and named based on their physical locations on chromosomes. All the VrBBXs were divided into five groups based on their phylogenetic relationships, the number of B-box they contained and whether there was an additional CONSTANS, CO-like and TOC1 (CCT) domain. Homology and collinearity analysis indicated that the BBX genes in mung bean and other species had undergone a relatively conservative evolution. Gene duplication analysis showed that only chromosomal segmental duplication contributed to the expansion of VrBBX genes and that most of the duplicated gene pairs experienced purifying selection pressure during evolution. Gene structure and motif analysis revealed that VrBBX genes clustered in the same group shared similar structural characteristics. An analysis of cis-acting elements indicated that elements related to stress and hormone responses were prevalent in the promoters of most VrBBXs. The RNA-seq data analysis and qRT-PCR of nine VrBBX genes demonstrated that VrBBX genes may play a role in response to environmental stress. Moreover, VrBBX5, VrBBX10 and VrBBX12 are important candidate genes for plant stress response.

CONCLUSIONS

In this study, we systematically analyzed the genomic characteristics and expression patterns of the BBX gene family under ABA, PEG and NaCl treatments. The results will help us better understand the complexity of the BBX gene family and provide valuable information for future functional characteristics of specific genes in this family.

Identification of phospholipase Ds and phospholipid species involved in circadian clock alterations using CRISPR/Cas9-based multiplex editing of Arabidopsis

Reciprocal regulation between the circadian clock and lipid metabolism is emerging, but its mechanisms remain elusive. We reported that a lipid metabolite phosphatidic acid (PA) bound to the core clock transcription factors LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and chemical suppression of phospholipase D (PLD)-catalyzed PA formation perturbed the clock in Arabidopsis. Here, we identified, among 12 members, specific PLDs critical to regulating clock function. We approached this using a multiplex CRISPR/Cas9 system to generate a library of plants bearing randomly mutated PLDs, then screening the mutants for altered rhythmic expression of CCA1 . All PLD s, except for β2 , were effectively edited, and the mutations were heritable. Screening of T2 plants identified some with an altered rhythm of CCA1 expression, and this trait was observed in many of their progenies. Genotyping revealed that at least two of six PLD s ( α1, α3 , γ1 , δ , ε and ζ2 ) were mutated in the clock-altered plants. Those plants also had reduced levels of PA molecular species that bound LHY and CCA1. This study identifies combinations of two or more PLDs and changes in particular phospholipid species involved in clock outputs and also suggests a functional redundancy of the six PLDs for regulating the plant circadian clock.

One sentence summary

This study identifies combinations of two or more phospholipase Ds involved in altering clock outputs and the specific phosphatidic acid species impacting the clock rhythms.

Flowering time regulator qFT13-3 involved in soybean adaptation to high latitudes

Soybean is a short-day plant that typically flowers earlier when exposed to short-day conditions. However, the identification of genes associated with earlier flowering time but without a yield penalty is rare. In this study, we conducted genome-wide association studies (GWAS) using two re-sequencing datasets that included 113 wild soybeans (G. soja) and 1192 cultivated soybeans (G. max), respectively, and simultaneously identified a candidate flowering gene, qFT13-3, which encodes a protein homologous to the pseudo-response regulator (PRR) transcription factor. We identified four major haplotypes of qFT13-3 in the natural population, with haplotype H4 (qFT13-3H4) being lost during domestication, while qFT13-3H1 underwent natural and artificial selection, increasing in proportion from 4.5% in G. soja to 43.8% in landrace and to 81.9% in improve cultivars. Notably, most cultivars harbouring qFT13-3H1 were located in high-latitude regions. Knockout of qFT13-3 accelerated flowering and maturity time under long-day conditions, indicating that qFT13-3 functions as a flowering inhibitor. Our results also showed that qFT13-3 directly downregulates the expression of GmELF3b-2 which is a component of the circadian clock evening complex. Field trials revealed that the qft13-3 mutants shorten the maturity period by 11 days without a concomitant penalty on yield. Collectively, qFT13-3 can be utilized for the breeding of high-yield cultivars with a short maturity time suitable for high latitudes.

Transcriptome Analysis of Intermittent Light Induced Early Bolting in Flowering Chinese Cabbage

In flowering Chinese cabbage, early booting is one of the most important characteristics that is linked with quality and production. Through fixed light intensity (280 μmol·m-2·s-1) and fixed intermittent lighting in flowering Chinese cabbage, there was early bolting, bud emergence, and flowering. Moreover, the aboveground fresh weight, blade area, dry weight of blade, and quantification of the leaves in flowering Chinese cabbage were significantly reduced, while the thickness of tillers, tillers height, dry weight of tillers, and tillers weight were significantly increased. The chlorophyll contents and soil-plant analysis and development (SPAD) value decreased in the early stage and increased in the later stage. The nitrate content decreased, while the photosynthetic rate, vitamin C content, soluble sugar content, soluble protein content, phenolic content, and flavonoid content increased, and mineral elements also accumulated. In order to explore the mechanism of intermittent light promoting the early bolting and flowering of '49d' flowering Chinese cabbage, this study analyzed the transcriptional regulation from a global perspective using RNA sequencing. A total of 17,086 differentially expressed genes (DEGs) were obtained and 396 DEGs were selected that were closely related to early bolting. These DEGs were mainly involved in pollen wall assembly and plant circadian rhythm pathways, light action (34 DEGs), hormone biosynthesis and regulation (26 DEGs), development (21 DEGs), and carbohydrate synthesis and transport (6 DEGs). Three hub genes with the highest connectivity were identified through weighted gene co-expression network analysis (WGCNA): BrRVE, BrLHY, and BrRVE1. It is speculated that they may be involved in the intermittent light regulation of early bolting in flowering Chinese cabbage. In conclusion, intermittent light can be used as a useful tool to regulate plant growth structure, increase planting density, enhance photosynthesis, increase mineral accumulation, accelerate growth, and shorten the breeding cycle.

Genome-wide identification and expression profiling of the ABI5 gene family in foxtail millet (Setaria italica)

BACKGROUND

ABA Insensitive 5 (ABI5) is a basic leucine zipper transcription factor that crucially influences plant growth, development, and stress response. However, there is minimal research on the ABI5 family in foxtail millet.

RESULTS

In this study, 16 ABI5 genes were identified in foxtail millet, and their sequence composition, gene structures, cis-acting elements, chromosome positions, and gene replication events were analyzed. To more thoroughly evaluate the developmental mechanisms of the SiABI5 family during evolution, we selected three dicotyledons (S. lycopersicum, A. thaliana, F. tataricum) and three (Z. mays, O. sativa, S. bicolor) specific representative monocotyledons associated with foxtail millet for comparative homology mapping. The results showed that foxtail millet ABI5 genes had the best homology with maize. A promoter sequence analysis showed that the SiABI5s contain numerous cis-acting elements related to hormone and stress responses, indicating that the regulation of SiABI5 expression was complex. The expression responses of 16 genes in different tissues, seed germination, and ear development were analyzed. A total of six representative genes were targeted from five subfamilies to characterize their gene expression responses to four different abiotic stresses. Overexpression of SiABI5.12 confers tolerance to osmotic stress in transgenic Arabidopsis thaliana, which demonstrated the function of SiABI5 responded to abiotic stress.

CONCLUSIONS

In summary, our research results comprehensively characterized the SiABI5 family and can provide a valuable reference for demonstrating the role of SiABI5s in regulating abiotic stress responses in foxtail millet.

Core clock genes adjust growth cessation time to day-night switches in poplar

Poplar trees use photoperiod as a precise seasonal indicator, synchronizing plant phenology with the environment. Daylength cue determines FLOWERING LOCUS T 2 (FT2) daily expression, crucial for shoot apex development and establishment of the annual growing period. However, limited evidence exists for the molecular factors controlling FT2 transcription and the conservation with the photoperiodic control of Arabidopsis flowering. We demonstrate that FT2 expression mediates growth cessation response quantitatively, and we provide a minimal data-driven model linking core clock genes to FT2 daily levels. GIGANTEA (GI) emerges as a critical inducer of the FT2 activation window, time-bound by TIMING OF CAB EXPRESSION (TOC1) and LATE ELONGATED HYPOCOTYL (LHY2) repressions. CRISPR/Cas9 loss-of-function lines validate these roles, identifying TOC1 as a long-sought FT2 repressor. Additionally, model simulations predict that FT2 downregulation upon daylength shortening results from a progressive narrowing of this activation window, driven by the phase shift observed in the preceding clock genes. This circadian-mediated mechanism enables poplar to exploit FT2 levels as an accurate daylength-meter.

Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops

MAIN CONCLUSION

Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. The circadian clock senses light and temperature in day-night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis. Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional-translational feedback loops involving morning (CCA1, LHY), mid-day (PRR9, PRR7, PRR5), and evening (TOC1, ELF3, ELF4, LUX) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis, maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene‒phytohormone‒trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops.

The interplay between the circadian clock and abiotic stress responses mediated by ABF3 and CCA1/LHY

Climate change is a global concern for all life on our planet, including humans and plants. Plants' growth and development are significantly affected by abiotic stresses, including adverse temperature, inadequate or excess water availability, nutrient deficiency, and salinity. The circadian clock is a master regulator of numerous developmental and metabolic processes in plants. In an effort to identify new clock-related genes and outputs through bioinformatic analysis, we have revealed that CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) play a crucial role in regulating a wide range of abiotic stress responses and target ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING FACTOR3 (ABF3), a key transcription factor in the plant hormone Abscisic acid (ABA)-signaling pathway. Specifically, we found that CCA1 and LHY regulate the expression of ABF3 under diel conditions, as well as seed germination under salinity. Conversely, ABF3 controls the expression of core clock genes and orchestrates the circadian period in a stress-responsive manner. ABF3 delivers the stress signal to the central oscillator by binding to the promoter of CCA1 and LHY. Overall, our study uncovers the reciprocal regulation between ABF3 and CCA1/LHY and molecular mechanisms underlying the interaction between the circadian clock and abiotic stress. This finding may aid in developing molecular and genetic solutions for plants to survive and thrive in the face of climate change.

Plants distinguish different photoperiods to independently control seasonal flowering and growth

Plants measure daylength (photoperiod) to regulate seasonal growth and flowering. Photoperiodic flowering has been well studied, but less is known about photoperiodic growth. By using a mutant with defects in photoperiodic growth, we identified a seasonal growth regulation pathway that functions in long days in parallel to the canonical long-day photoperiod flowering mechanism. This is achieved by using distinct mechanisms to detect different photoperiods: The flowering pathway measures photoperiod as the duration of light intensity, whereas the growth pathway measures photoperiod as the duration of photosynthetic activity (photosynthetic period). Plants can then independently control expression of genes required for flowering or growth. This demonstrates that seasonal flowering and growth are dissociable, allowing them to be coordinated independently across seasons.

Evolution and Dynamic Transcriptome of Key Genes of Photoperiodic Flowering Pathway in Water Spinach (Ipomoea aquatica)

The photoperiod is a major environmental factor in flowering control. Water spinach flowering under the inductive short-day condition decreases the yield of vegetative tissues and the eating quality. To obtain an insight into the molecular mechanism of the photoperiod-dependent regulation of the flowering time in water spinach, we performed transcriptome sequencing on water spinach under long- and short-day conditions with eight time points. Our results indicated that there were 6615 circadian-rhythm-related genes under the long-day condition and 8691 under the short-day condition. The three key circadian-rhythm genes, IaCCA1, IaLHY, and IaTOC1, still maintained single copies and similar IaCCA1, IaLHY, and IaTOC1 feedback expression patterns, indicating the conservation of reverse feedback. In the photoperiod pathway, highly conserved GI genes were amplified into two copies (IaGI1 and IaGI2) in water spinach. The significant difference in the expression of the two genes indicates functional diversity. Although the photoperiod core gene FT was duplicated to three copies in water spinach, only IaFT1 was highly expressed and strongly responsive to the photoperiod and circadian rhythms, and the almost complete inhibition of IaFT1 in water spinach may be the reason why water spinach does not bloom, no matter how long it lasts under the long-day condition. Differing from other species (I. nil, I. triloba, I. trifida) of the Ipomoea genus that have three CO members, water spinach lacks one of them, and the other two CO genes (IaCO1 and IaCO2) encode only one CCT domain. In addition, through weighted correlation network analysis (WGCNA), some transcription factors closely related to the photoperiod pathway were obtained. This work provides valuable data for further in-depth analyses of the molecular regulation of the flowering time in water spinach and the Ipomoea genus.

Phosphatidic acid signaling and function in nuclei

Membrane lipidomes are dynamic and their changes generate lipid mediators affecting various biological processes. Phosphatidic acid (PA) has emerged as an important class of lipid mediators involved in a wide range of cellular and physiological responses in plants, animals, and microbes. The regulatory functions of PA have been studied primarily outside the nuclei, but an increasing number of recent studies indicates that some of the PA effects result from its action in nuclei. PA levels in nuclei are dynamic in response to stimuli. Changes in nuclear PA levels can result from activities of enzymes associated with nuclei and/or from movements of PA generated extranuclearly. PA has also been found to interact with proteins involved in nuclear functions, such as transcription factors and proteins undergoing nuclear translocation in response to stimuli. The nuclear action of PA affects various aspects of plant growth, development, and response to stress and environmental changes.

Circadian clock factors regulate the first condensation reaction of fatty acid synthesis in Arabidopsis

The circadian clock regulates temporal metabolic activities, but how it affects lipid metabolism is poorly understood. Here, we show that the central clock regulators LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) regulate the initial step of fatty acid (FA) biosynthesis in Arabidopsis. Triacylglycerol (TAG) accumulation in seeds was increased in LHY-overexpressing (LHY-OE) and decreased in lhycca1 plants. Metabolic tracking of lipids in developing seeds indicated that LHY enhanced FA synthesis. Transcript analysis revealed that the expression of genes involved in FA synthesis, including the one encoding β-ketoacyl-ACP synthase III (KASIII), was oppositely changed in developing seeds of LHY/CCA1-OEs and lhycca1. Chromatin immunoprecipitation, electrophoretic mobility shift, and transactivation assays indicated that LHY bound and activated the promoter of KASIII. Furthermore, phosphatidic acid, a metabolic precursor to TAG, inhibited LHY binding to KASIII promoter elements. Our data show a regulatory mechanism for plant lipid biosynthesis by the molecular clock.

Loss of Diel Circadian Clock Gene Cycling Is a Part of Grape Berry Ripening

Diel cycles of gene expression are thought to adapt plants to 24-h changes in environmental conditions. The circadian clock contributes to this process, but less is known about circadian programs in developing reproductive organs. While model plants and controlled conditions have contributed greatly to our knowledge of circadian clock function, there is a need to better understand its role in crop plants under field conditions with fluctuating light and temperature. In this study, we investigated changes in the circadian clock during the development of grape berries of Vitis vinifera L. We found that the transcripts of circadian clock homologs had high-amplitude oscillations prior to, but not during, ripening. As ripening progressed, the amplitude and rhythmicity of the diel oscillations decreased until most transcripts tested had no significant fluctuation over the 24-h cycle. Despite this loss of rhythmicity, the majority of circadian clock genes investigated were expressed at or near their abundance at the nadir of their pre-ripening oscillation although the berries remained transcriptionally active. From this, it can be concluded that cycling of the canonical circadian clock appears unnecessary for berry ripening. Our data suggest that changes in circadian clock dynamics during reproductive organ development may have important functional consequences.

The Roles of the PSEUDO-RESPONSE REGULATORs in Circadian Clock and Flowering Time in Medicago truncatula

PSEUDO-RESPONSE REGULATORs (PRRs) play key roles in the circadian rhythms and flowering in plants. Here, we identified the four members of the PRR family in Medicago truncatula, including MtPRR9a, MtPRR9b, MtPRR7 and MtPRR5, and isolated their Tnt1 retrotransposon-tagged mutants. They were expressed in different organs and were nuclear-localized. The four MtPRRs genes played important roles in normal clock rhythmicity maintenance by negatively regulating the expression of MtGI and MtLHY. Surprisingly, the four MtPRRs functioned redundantly in regulating flowering time under long-day conditions, and the quadruple mutant flowered earlier. Moreover, MtPRR can recruit the MtTPL/MtTPR corepressors and the other MtPRRs to form heterodimers to constitute the core mechanism of the circadian oscillator.

Circadian regulation of metabolism across photosynthetic organisms

Circadian regulation produces a biological measure of time within cells. The daily cycle in the availability of light for photosynthesis causes dramatic changes in biochemical processes in photosynthetic organisms, with the circadian clock having crucial roles in adaptation to these fluctuating conditions. Correct alignment between the circadian clock and environmental day-night cycles maximizes plant productivity through its regulation of metabolism. Therefore, the processes that integrate circadian regulation with metabolism are key to understanding how the circadian clock contributes to plant productivity. This forms an important part of exploiting knowledge of circadian regulation to enhance sustainable crop production. Here, we examine the roles of circadian regulation in metabolic processes in source and sink organ structures of Arabidopsis. We also evaluate possible roles for circadian regulation in root exudation processes that deposit carbon into the soil, and the nature of the rhythmic interactions between plants and their associated microbial communities. Finally, we examine shared and differing aspects of the circadian regulation of metabolism between Arabidopsis and other model photosynthetic organisms, and between circadian control of metabolism in photosynthetic and non-photosynthetic organisms. This synthesis identifies a variety of future research topics, including a focus on metabolic processes that underlie biotic interactions within ecosystems.

An interview with Joshua Gendron

Joshua Gendron is Associate Professor of Molecular, Cellular and Developmental Biology at Yale University, USA. His research focuses on understanding how protein degradation systems regulate timing mechanisms and environment sensing in plants. Joshua joined the team at Development as a Guest Editor for the journal's Special Issue: Metabolic and Nutritional Control of Development and Regeneration. We met with him over Teams to learn more about why he decided to get involved, his research and his career path.

Myb-like transcription factors have epistatic effects on circadian clock function but additive effects on plant growth

The functions of closely related Myb-like repressor and Myb-like activator proteins within the plant circadian oscillator have been well-studied as separate groups, but the genetic interactions between them are less clear. We hypothesized that these repressors and activators would interact additively to regulate both circadian and growth phenotypes. We used CRISPR-Cas9 to generate new mutant alleles and performed physiological and molecular characterization of plant mutants for five of these core Myb-like clock factors compared with a repressor mutant and an activator mutant. We first examined circadian clock function in plants likely null for both the repressor proteins, CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), and the activator proteins, REVEILLE 4 (RVE4), REVEILLE (RVE6), and REVEILLE (RVE8). The rve468 triple mutant has a long period and flowers late, while cca1 lhy rve468 quintuple mutants, similarly to cca1 lhy mutants, have poor circadian rhythms and flower early. This suggests that CCA1 and LHY are epistatic to RVE4, RVE6, and RVE8 for circadian clock and flowering time function. We next examined hypocotyl elongation and rosette leaf size in these mutants. The cca1 lhy rve468 mutants have growth phenotypes intermediate between cca1 lhy and rve468 mutants, suggesting that CCA1, LHY, RVE4, RVE6, and RVE8 interact additively to regulate growth. Together, our data suggest that these five Myb-like factors interact differently in regulation of the circadian clock versus growth. More generally, the near-norm al seedling phenotypes observed in the largely arrhythmic quintuple mutant demonstrate that circadian-regulated output processes, like control of hypocotyl elongation, do not always depend upon rhythmic oscillator function.

The circadian clock regulates PIF3 protein stability in parallel to red light

The circadian clock is an endogenous oscillator, but its importance lies in its ability to impart rhythmicity on downstream biological processes or outputs. Focus has been placed on understanding the core transcription factors of the circadian clock and how they connect to outputs through regulated gene transcription. However, far less is known about posttranslational mechanisms that tether clocks to output processes through protein regulation. Here, we identify a protein degradation mechanism that tethers the clock to photomorphogenic growth. By performing a reverse genetic screen, we identify a clock-regulated F-box type E3 ubiquitin ligase, CLOCK-REGULATED F-BOX WITH A LONG HYPOCOTYL 1 ( CFH1 ), that controls hypocotyl length. We then show that CFH1 functions in parallel to red light signaling to target the transcription factor PIF3 for degradation. This work demonstrates that the circadian clock is tethered to photomorphogenesis through the ubiquitin proteasome system and that PIF3 protein stability acts as a hub to integrate information from multiple environmental signals.

Characterizing the circadian connectome of Ocimum tenuiflorum using an integrated network theoretic framework

Across the three domains of life, circadian clock is known to regulate vital physiological processes, like, growth, development, defence etc. by anticipating environmental cues. In this work, we report an integrated network theoretic methodology comprising of random walk with restart and graphlet degree vectors to characterize genome wide core circadian clock and clock associated raw candidate proteins in a plant for which protein interaction information is available. As a case study, we have implemented this framework in Ocimum tenuiflorum (Tulsi); one of the most valuable medicinal plants that has been utilized since ancient times in the management of a large number of diseases. For that, 24 core clock (CC) proteins were mined in 56 template plant genomes to build their hidden Markov models (HMMs). These HMMs were then used to identify 24 core clock proteins in O. tenuiflorum. The local topology of the interologous Tulsi protein interaction network was explored to predict the CC associated raw candidate proteins. Statistical and biological significance of the raw candidates was determined using permutation and enrichment tests. A total of 66 putative CC associated proteins were identified and their functional annotation was performed.

OsTOC1 plays dual roles in the regulation of plant circadian clock by functioning as a direct transcription activator or repressor

Plant clock function relies on precise timing of gene expression through complex regulatory networks consisting of activators and repressors at the core of oscillators. Although TIMING OF CAB EXPRESSION 1 (TOC1) has been recognized as a repressor involved in shaping oscillations and regulating clock-driven processes, its potential to directly activate gene expression remains unclear. In this study, we find that OsTOC1 primarily acts as a transcriptional repressor for core clock components, including OsLHY and OsGI. Here, we show that OsTOC1 possesses the ability to directly activate the expression of circadian target genes. Through binding to the promoters of OsTGAL3a/b, transient activation of OsTOC1 induces the expression of OsTGAL3a/b, indicating its role as an activator contributing to pathogen resistance. Moreover, TOC1 participates in regulating multiple yield-related traits in rice. These findings suggest that TOC1's function as a transcriptional repressor is not inherent, providing flexibility to circadian regulations, particularly in outputs.

ZmGI2 regulates flowering time through multiple flower development pathways in maize

GIGANTEA (GI) encodes a component of the circadian clock core oscillator and has been identified as a regulatory pathway of the circadian rhythm and photoperiodic flowering in model plants. However, the regulatory pathway of GI affecting flowering time is unknown in maize. Here, we identified that the zmgi2 mutant flowered earlier than the wild type under long day (LD) conditions, whereas the difference in flowering time was not apparent under short day (SD) conditions. The 24 h optimal expression of the gene in the stem apex meristems (SAM) appeared at 9 h after dawn under LD conditions and at 11 h after dawn under SD conditions. DAP-Seq and RNA-Seq further revealed that ZmGI2 delays flowering by directly binding to the upstream regions of ZmVOZs, ZmZCN8 and ZmFPF1 to repress the expression of these genes and by directly binding to the upstream regions of ZmARR11, ZmDOF and ZmUBC11 to promote the expression of these genes. The genetic and biochemical evidence suggests a model for the potential role of ZmGI2 in regulating the flowering time-dependent photoperiodic pathway. This study provides novel insights into the function of ZmGIs in maize and further demonstrates their potential importance for floral transition. These results contribute to a comprehensive understanding of the molecular mechanisms and regulatory networks of GI transcription factors in regulating flowering time in maize.