CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses

The association between GABA-shunt and circadian rhythm directs salt stress responses in Nicotiana tabaccum L

Gamma amino butyric acid (GABA) is a neurotransmitter inhibitor molecule functioning in the central nervous system of mammals, found in all the suprachiasmatic nucleus (SCN) and has a critical role in refining circadian rhythm since the SCN sends signals to peripheral clocks for synchronization. GABA may function in plants in a similar way to animals in relation to circadian rhythm. Previously, we found that GABA biosynthesis was affected at transcriptional level in Nicotiana tabaccum under drought stress during 24 h periodicity. In the light of these findings we hypothesized that, GABA might be an internal cue for circadian rhythm and disruption of this interaction by different stresses might affect phase rhythms in tobacco. We conducted experiments with N. tabaccum plants under salt stress in 72 h periodicity. Physiological parameters along with GABA content, GAD and GABA-T activities were measured and the transcript profiles of genes related to the morning, central and evening loops of the circadian rhythm were also analyzed. According to our findings, under control conditions, GABA-shunt was found to be associated with CCA1, PRR7, TOC, PRR3 and GI, while H2O2 content was negatively correlated with GABA catabolism. Salt stress reversed the daily rhythm of GABA biosynthesis (day and night cycle) as compared to the control plants. The morning and the night/central genes' transcript abundances were impaired during day-night transitions in salt-stressed groups. Moreover, under salt stress, GABA catabolism was associated more with the morning phase genes and the correlation between GABA-shunt and the circadian rhythm was adversely affected. It is possible that increased H2O2 content under salt stress may also play a regulatory role in this interplay.

GIGANTEA functions as a co-repressor of cold stress response with a histone-modifying complex

The circadian clock in plants is crucial for regulating stress responses, including cold tolerance. Cold stress induces the expression of C-REPEAT BINDING FACTOR (CBF) transcription factors, which activate COLD-REGULATED (COR) genes to mitigate cold-induced damage. Previously, we identified that HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE15 (HOS15)-HISTONE DEACETYLASE 2C (HD2C) complex regulates cold tolerance by modulating histone deacetylation on the COR genes. Our research reports that the circadian oscillator GIGANTEA (GI) regulates the association of histone deacetylase complex on the COR promoter, controlling cold tolerance. We show that GI functions downstream of HOS15, as the hos15-2 gi-2 double mutant exhibits freezing tolerance and expression of the COR gene like gi-2. Consistent with the HOS15, GI doesn't affect CBF transcription, suggesting that GI involved cold stress responses through HOS15-mediated COR gene regulation. Moreover, GI reduces histone acetylation and CBF binding at the COR15A promoter under cold stress, repressing COR15A gene expression. We further demonstrate that GI forms a co-repressor with HOS15 and HD2C, inhibiting CBF binding and preventing COR gene activation under normal conditions. These findings provide insights into molecular mechanisms by which GI, HOS15, and HD2C coordinate cold stress responses, offering potential strategies for enhancing plant cold tolerance through chromatin-mediated regulation.

Influence of arsenic exposure on the daily changes of glycerophospholipid turnover and assessment of defence mechanisms in tobacco hairy roots

Arsenic (As) affects several key physiological and metabolic processes, resulting in reduced seed germination and plant growth. The aim of this work was to study the impact of arsenite (AsIII) treatment on the metabolism of glycerophospholipids (MGPLs), evaluating the turnover activity (TA) of major GPLs, the expression of genes involved in this metabolism and also related to stress response. Total antioxidant activity (TAA) under AsIII-induced stress was evaluated as well as the implication of the circadian clock (CC) on the parameters studied. For this purpose, tobacco (Nicotiana tabacum) hairy roots (HRs) synchronized with a 12/12 h light/dark photoperiod were used. The TA of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) showed a circadian behavior, especially under untreated conditions. However, the As treatment significantly modified the TA profiles of all analyzed GPLs, by inducing an opposite oscillation (PC and LysoPC) or increasing their TA (LysoPE and cardiolipin) during both the light and dark phase. Curiously, under As-treatment, the relative expression of key genes involved in the MGPLs (NtLPAT2 and NtCEK4) was increased and showed a circadian oscillation, while under control conditions, no significant changes were detected. NtPHT4;1 gene, involved in As-induced stress, showed a circadian expression profile, which was conserved under AsIII treatment but with an antiphase performance. Moreover, TAA was significantly affected in AsIII-treated HRs, mainly during the dark phase. Our results show that AsIII treatment affected the parameters studied and constitute valuable evidence to unravel the plant responses and the CC implication under AsIII-induced stress.

Circadian Biology in Obstructive Sleep Apnea-Associated Cardiovascular Disease

A dysregulated circadian system is independently associated with both Obstructive Sleep Apnea (OSA) and cardiovascular disease (CVD). OSA and CVD coexistence is often seen in patients with prolonged untreated OSA. However, the role of circadian dysregulation in their relationship is unclear. Half of the human genes, associated biological pathways, and physiological functions exhibit circadian rhythms, including blood pressure and heart rate regulation. Mechanisms related to circadian dysregulation and heart function are potentially involved in the coexistence of OSA and CVD. In this article, we provide a comprehensive overview of circadian dysregulation in OSA and associated CVD. We also discuss feasible animal models and new avenues for future research to understand their relationship. Oxygen-sensing pathways, inflammation, dysregulation of cardiovascular processes, oxidative stress, metabolic regulation, hormone signaling, and epigenetics are potential clock-regulated mechanisms connecting OSA and CVD.

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.

The core morning clock component CCA1 enhances UPR target gene expression to facilitate ER stress recovery

The endoplasmic reticulum (ER) is a cellular organelle responsible for protein synthesis and folding. When its protein folding capacity is exceeded, unfolded or misfolded proteins accumulate, causing ER stress and triggering the unfolded protein response (UPR) to restore ER proteostasis. Although UPR gene expression in plants follows a diel cycle, the mechanisms by which the circadian clock regulates these genes remain unclear. Here, we demonstrate that sensitivity to ER stress in root growth exhibits time-of-day phases and that the circadian clock regulates UPR target gene expression during ER stress. Notably, mutations in the core morning clock component CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) impair ER stress recovery. CCA1 forms a complex with the UPR modulator basic leucine zipper 28 (bZIP28) and acts as an upstream regulator of ER stress recovery. Upon ER stress, CCA1 is stabilized and associates with bZIP28 at the ER stress response element within the BiP3 promoter, enhancing the ER stress response. Thus, CCA1 and bZIP28 coordinate a time-dependent adaptive response to ER stress to maintain ER proteostasis. Our results suggest that the circadian clock primes the timing and levels of ER chaperone expression to enhance ER stress tolerance.

New insights on the impact of light, photoperiod and temperature on the reproduction of green algae Ulva prolifera via transcriptomics and physiological analyses

Ulva prolifera, a key species in China's massive green tides, is widely used in aquaculture, biofuel, pharmaceutical and cosmetic industries. In this study, we cultured U. prolifera under 100, 200, and 400 μmol m-2 s-1 with 10:14 and 12:12 light/dark at 15 °C and 25 °C, respectively, to investigate the effectiveness of light intensity, photoperiod, and temperature on the reproduction cell formation, oxidative status, photosynthesis on this species, as well as the related genes from transcriptomic perspective. Results showed that 25 °C or 400 μmol m-2 s-1 increased reproduction, although shorter daylength reduced cell numbers, correlating with higher O₂- content. The ascorbate-glutathione cycle activity was enhanced by reproduction, aligning with gene expression changes. Meiosis-specific gene MSH4 expression correlated positively with cell numbers. We speculate that higher temperature, light intensity, and shorter photoperiod enhance reproduction by inducing oxidative stress and signaling via the AsA-GSH cycle to regulate MSH4 expression.

Circadian clock regulation in soybean senescence: a transcriptome analysis of early and late senescence types

BACKGROUND

Plant senescence is the process of physiological maturation of plants and is important for crop yield and quality. Senescence is controlled by several factors, such as temperature and photoperiod. However, the molecular basis by which these genes promote senescence in soybeans is not well understood. We identified senescence-related genes via transcriptome analysis of early-senescence (ES)- and late-senescence (LS)-type plants to elucidate the molecular mechanisms of senescence in soybeans.

RESULTS

We obtained early-senescence (ES)- and late-senescence (LS)-type F7 plants from a cross between a hybrid (Glycine max × Glycine soja) and the Glycine max cultivar. The ES-type plants presented the reproductive (R2) growth stage at 50 days after sowing (DAS) and the R7 growth stage at 95 DAS, whereas the LS-type plants presented the beginning of the R1 and R6 growth stages at 50 and 95 DAS, respectively. To understand the molecular mechanisms underlying this senescence, we performed transcriptome analysis of leaves from 50 to 95 DAS of ES- and LS-type plants. A total of 2,414 and 2,471 genes at 50 and 95 DAS, respectively, were differentially expressed between ES-type and LS-type plants. Twenty-three candidate genes associated with the circadian clock, chlorophyll biosynthesis, phytohormones, and senescence-associated protein kinases were identified, and their expression levels were analyzed. In addition, to understand interaction between circadian clock and senescence, we analyzed expression patterns of seven circadian clock-related genes during the time period (light and dark condition): CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), CONSTANS-LIKE 9 (COL9), LUX ARRHYTHMO (LUX) EARLY FLOWERING 3 (ELF3), PSEUDO-RESPONSE REGULATOR5 (PRR5) and GIGANTEA (GI). The expression patterns of circadian clock-related genes were similar in the ES- and LS-type plants. However, the transcription levels of these genes were compared between ES- and LS-type plants, and the expression of these genes was greater than that in LS-type plants during the period when expression increased. Therefore, each set of candidate genes regulated senescence in each plant by regulating their expression level.

CONCLUSIONS

These findings provide novel insights into the regulation of senescence in soybean plants, which could lead to the development of new strategies to improve agriculture.

Proline and ROS: A Unified Mechanism in Plant Development and Stress Response?

The proteinogenic amino acid proline plays crucial roles in both plant development and stress responses, far exceeding its role in protein synthesis. However, the molecular mechanisms and the relative importance of these additional functions of proline remain under study. It is well documented that both stress responses and developmental processes are associated with proline accumulation. Under stress conditions, proline is believed to confer stress tolerance, while under physiological conditions, it assists in developmental processes, particularly during the reproductive phase. Due to proline's properties as a compatible osmolyte and potential reactive oxygen species (ROS) scavenger, most of its beneficial effects have historically been attributed to the physicochemical consequences of its accumulation in plants. However, emerging evidence points to proline metabolism as the primary driver of these beneficial effects. Recent reports have shown that proline metabolism, in addition to supporting reproductive development, can modulate root meristem size by controlling ROS accumulation and distribution in the root meristem. The dynamic interplay between proline and ROS highlights a sophisticated regulatory network essential for plant resilience and survival. This fine-tuning mechanism, enabled by the pro-oxidant and antioxidant properties of compartmentalized proline metabolism, can modulate redox balance and ROS homeostasis, potentially explaining many of the multiple roles attributed to proline. This review uniquely integrates recent findings on the dual role of proline in both ROS scavenging and signaling, provides an updated overview of the most recent research published to date, and proposes a unified mechanism that could account for many of the multiple roles assigned to proline in plant development and stress defense. By focusing on the interplay between proline and ROS, we aim to provide a comprehensive understanding of this proposed mechanism and highlight the potential applications in improving crop resilience to environmental stress. Additionally, we address current gaps in understanding and suggest future research directions to further elucidate the complex roles of proline in plant biology.

Sleep disturbances and female infertility: a systematic review

BACKGROUND

Sleep disturbances are more prevalent among women with infertility. Current research increasingly highlights the significant relationship between sleep disturbances and female infertility, suggesting that sleep may be a key factor in reproductive health. In this review, we aim to delve into the complex interplay between sleep disturbances and female infertility, as well as to assess the underlying mechanisms involved, and seek to illuminate the causes of sleep-related fertility issues. The understanding of these contents may help clinicians enhance clinical strategies for managing sleep disturbances in women facing infertility challenges and provide timely support to those seeking fertility treatments.

METHODS

A comprehensive literature search was conducted in the PubMed and EMBASE databases. Studies that described sleep patterns or any type of sleep disturbance, sleep breathing disorders and their associations with female infertility or female fecundity, published between January 1, 2010, and November 1, 2023, were identified and extracted. The screening, data extraction, and quality assessment processes were independently performed by paired reviewers. The quality of the included studies was assessed using the Joanna Briggs Institute (JBI) Critical Appraisal tools for observational and cohort studies.

RESULTS

A total of 1,179 articles were initially identified from the search strategy (PubMed, n = 377; EMBASE, n = 802). After removing duplicates (n = 83) and screening for eligibility (n = 75), 19 studies were reviewed and determined to be eligible for inclusion. Infertile women generally report poorer sleep quality and exhibit more evening sleep chronotypes. Sleep disorders are significantly associated with infertility. Poor sleep quality, extreme sleep durations, and certain sleep chronotypes are associated with poorer fertility treatment outcomes, such as a reduced number of retrieved oocytes, decreased embryo quality, and lower fertilization rates. Obstructive sleep apnea (OSA) is also more prevalent in women with fertility issues, especially those with polycystic ovary syndrome (PCOS), and may negatively impact reproductive outcomes. The circadian rhythms of the Clock gene system, melatonin and hormone dysregulation, oxidative stress and immune response are considered to be potential mechanisms explaining how sleep disturbance impairs reproductive function, remain to be fully elucidated, and therefore, require further investigation.

CONCLUSIONS

Sleep disturbances are negatively associated with female infertility and poor fertility treatment outcomes. Longitudinal studies are expected to substantiate these findings and inform more nuanced approaches to prior sleep management and lifestyle advisement for infertile women, especially those undergoing fertility treatments.

TRIAL REGISTRATION

This study was registered in the International Prospective Register of Systematic Reviews (PROSPERO, #CRD42024498443).

Inflammation and DNA methylation in Alzheimer's disease: mechanisms of epigenetic remodelling by immune cell oxidants in the ageing brain

Alzheimer's disease is a neurodegenerative disease involving memory impairment, confusion, and behavioural changes. The disease is characterised by the accumulation of amyloid beta plaques and neurofibrillary tangles in the brain, which disrupt normal neuronal function. There is no known cure for Alzheimer's disease and due to increasing life expectancy, occurrence is projected to rise over the coming decades. The causes of Alzheimer's disease are multifactorial with inflammation, oxidative stress, genetic and epigenetic variation, and cerebrovascular abnormalities among the strongest contributors. We review the current literature surrounding inflammation and epigenetics in Alzheimer's disease, with a focus on how oxidants from infiltrating immune cells have the potential to alter DNA methylation profiles in the ageing brain.

Heat-inactivated Streptococcus pneumoniae augments circadian clock gene expression in zebrafish cells

The circadian clock is a cell-autonomous process that regulates daily internal rhythms by interacting with environmental signals. Reports across species show that infection can alter the expression of circadian genes; however, in teleosts, these effects are influenced by light exposure. Currently, no reports analyze the direct effects of bacterial exposure on the zebrafish clock. Using zebrafish Z3 cells, we demonstrate that exposure to heat-killed Streptococcus pneumoniae (HK-Spn) augments the expression of core repressive factors in a light- and time-dependent manner. In constant darkness, HK-Spn highly upregulated cry1a, per3, and per1b expression. In the presence of light, HK-Spn exposure rapidly and strongly upregulated per2 and cry1a, and this was proportionally increased with light intensity. The combinatorial effect of light and HK-Spn on per2 and cry1a was not duplicated with H2O2, a known byproduct of light exposure. However, the ROS inhibitor N-acetyl cysteine was sufficient to block HK-Spn augmentation of per2, cry1a, and per3. These findings demonstrate that exposure to an inactive bacteria influences the expression of zebrafish clock genes under different light conditions.

Photorespiratory Metabolism and Its Regulatory Links to Plant Defence Against Pathogens

When plants face biotic stress, the induction of defence responses imposes a massive demand for carbon and energy resources, which could decrease the reserves allocated towards growth. These growth-defence trade-offs have important implications for plant fitness and productivity and influence the outcome of plant-pathogen interactions. Biotic stress strongly affects plant cells' primary metabolism, including photosynthesis and respiration, the main source of energy and carbon skeletons for plant growth, development, and defence. Although the nature of photosynthetic limitations imposed by pathogens is variable, infection often increases photorespiratory pressure, generating conditions that promote ribulose-1,5-bisphosphate oxygenation, leading to a metabolic shift from assimilation to photorespiration. Photorespiration, the significant metabolic flux following photosynthesis, protects the photosynthetic apparatus from photoinhibition. However, recent studies reveal that its role is far beyond photoprotection. The intermediates of the photorespiratory cycle regulate photosynthesis, and photorespiration interacts with the metabolic pathways of nitrogen and sulphur, shaping the primary metabolism for stress responses. This work aims to present recent insights into the integration of photorespiration within the network of primary metabolism under biotic stress. It also explores the potential implications of regulating photosynthetic-photorespiratory metabolism for plant defence against bacterial and fungal pathogens.

Natural variation in LONELY GUY-Like 1 regulates rice grain weight under warmer night conditions

Global nighttime temperatures are rising at twice the rate of daytime temperatures and pose a challenge for rice (Oryza sativa) production. High nighttime temperature (HNT) stress affects rice yield by reducing grain weight, size, and fertility. Although the genes associated with these yield parameters have been identified and characterized under normal temperatures, the genetic basis of grain weight regulation under HNT stress remains less explored. We examined the natural variation for rice single grain weight (SGW) under HNT stress imposed during grain development. A genome-wide association analysis identified several loci associated with grain weight under HNT stress. A locus, SGW1, specific to HNT conditions resolved to LONELY GUY-Like 1 (LOGL1), which encodes a putative cytokinin-activation enzyme. We demonstrated that LOGL1 contributes to allelic variation at SGW1. Accessions with lower LOGL1 transcript abundance had higher grain weight under HNT. This was supported by the higher grain weight of logl1-mutants relative to the wild type under HNT. Compared to logl1-mutants, LOGL1 over-expressers showed increased sensitivity to HNT. We showed that LOGL1 regulates the thiamin biosynthesis pathway, which is under circadian regulation, which in turn is likely perturbed by HNT stress. These findings provide a genetic source to enhance rice adaptation to warming night temperatures and improve our mechanistic understanding of HNT stress tolerance pathways.

Genome-wide analysis of MYB transcription factor family and AsMYB1R subfamily contribution to ROS homeostasis regulation in Avena sativa under PEG-induced drought stress

BACKGROUND

The myeloblastosis (MYB) transcription factor (TF) family is one of the largest and most important TF families in plants, playing an important role in a life cycle and abiotic stress.

RESULTS

In this study, 268 Avena sativa MYB (AsMYB) TFs from Avena sativa were identified and named according to their order of location on the chromosomes, respectively. Phylogenetic analysis of the AsMYB and Arabidopsis MYB proteins were performed to determine their homology, the AsMYB1R proteins were classified into 5 subgroups, and the AsMYB2R proteins were classified into 34 subgroups. The conserved domains and gene structure were highly conserved among the subgroups. Eight differentially expressed AsMYB genes were screened in the transcriptome of transcriptional data and validated through RT-qPCR. Three genes in AsMYB2R subgroup, which are related to the shortened growth period, stomatal closure, and nutrient and water transport by PEG-induced drought stress, were investigated in more details. The AsMYB1R subgroup genes LHY and REV 1, together with GST, regulate ROS homeostasis to ensure ROS signal transduction and scavenge excess ROS to avoid oxidative damage.

CONCLUSION

The results of this study confirmed that the AsMYB TFs family is involved in the homeostatic regulation of ROS under drought stress. This lays the foundation for further investigating the involvement of the AsMYB TFs family in regulating A. sativa drought response mechanisms.

A coupled model between circadian, cell-cycle, and redox rhythms reveals their regulation of oxidative stress

Most organisms possess three biological oscillators, circadian clock, cell cycle, and redox rhythm, which are autonomous but interact each other. However, whether their interactions and autonomy are beneficial for organisms remains unclear. Here, we modeled a coupled oscillator system where each oscillator affected the phase of the other oscillators. We found that multiple types of coupling prevent a high H2O2 level in cells at M phase. Consequently, we hypothesized a high H2O2 sensitivity at the M phase and found that moderate coupling reduced cell damage due to oxidative stress by generating appropriate phase relationships between three rhythms, whereas strong coupling resulted in an elevated cell damage by increasing the average H2O2 level and disrupted the cell cycle. Furthermore, the multicellularity model revealed that phase variations among cells confer flexibility in synchronization with environments at the expense of adaptability to the optimal environment. Thus, both autonomy and synchrony among the oscillators are important for coordinating their phase relationships to minimize oxidative stress, and couplings balance them depending on environments.

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.

Physiological and multi-omics analysis reveals the influence of copper on Halophila beccarii Asch

High concentrations of copper can pollute coastal waters, primarily from agricultural runoff and mining activities, which can harm marine organisms, including seagrasses. The molecular mechanism of copper toxicity to seagrass currently remains unclear. To determine the response to copper, physiological and multi-omic analyses were conducted to explore the molecular mechanism by which copper affects the global threatened seagrass Halophila beccarii Asch. Excessive copper stress causes oxidative damage and stimulates the activity of the antioxidant enzyme system to remove excess reactive oxygen species (ROS), thereby reducing the damage caused by copper stress. Cu increases the activities of superoxide dismutase (EC 1.15.1.1), catalase (EC 1.11.1.6), peroxidase (EC 1.11.1.7), ascorbate peroxidase (EC 1.11.1.11), glutathione peroxidase (EC 1.11.1.9), ascorbate oxidase (EC 1.10.3.3), glutathione reductase (EC 1.6.4.2), and dehydroascorbate reductase (EC 1.8.5.1) and the content of malondialdehyde and reduces the activity of monodehydroascorbate reductase (EC 1.6.5.4). Under copper stress, H. beccarii upregulates the metabolic pathways of steroid biosynthesis and cutin, suberin, and wax biosynthesis, downregulates the metabolic pathways of arginine and proline metabolism and fructose and mannose metabolism; the levels of expression of the ribosome-related genes; upregulates the levels of expression of circadian rhythm-related proteins and downregulates the levels of glutathione metabolism and the proteins related to carbon fixation. This study provides new insights into the response of seagrass to copper stress and reports potential candidate metabolites, genes, and proteins that can be considered as biomarkers to improve the protection and management of seagrass meadows.

Tomato and mini-cucumber tolerance to photoperiodic injury involves photorespiration and the engagement of nighttime cyclic electron flow from dynamic LEDs

Controlled environment agriculture (CEA) is critical for achieving year-round food security in many regions of the world. CEA is a resource-intensive endeavor, with lighting consuming a large fraction of the energy. To lessen the burden on the grid and save costs, an extended photoperiod strategy can take advantage of off-peak time-of-day options from utility suppliers. However, extending the photoperiod limits crop production morphologically and physiologically if pushed too long. Here, we present a continuous-light dynamic light-emitting diode (LED) strategy (involving changes in spectra, intensity, and timing), that overcomes these limitations. We focused on tomato, a well described photoperiodic injury-sensitive species, and mini-cucumber, a photoperiodic injury-tolerant species to first assess morphological responses under control (16-h photoperiod, unchanging spectrum), constant (24-h photoperiod, unchanging spectrum), and two variations of a dynamic LED strategy, dynamic 1 (16-h "day", 3-h "peak", 8-h "night" spectra) and dynamic 2 (20-h "day", 5-h "peak", 4-h "night" spectra). Next, we tested the hypothesis of photorespiration's involvement in photoperiodic injury by using a leaf gas exchange coupled with chlorophyll fluorescence protocol. We further explored Adenosine triphosphate (ATP): Nicotinamide adenine dinucleotide phosphate (NADPH) ratio supply/demand responses by probing photosynthetic electron flow and proton flow with the MultispeQ instrument. We found canopy architecture can be tuned by minor variations of the same dynamic LED strategy, and we highlight dynamic 1 as the optimal choice for both tomato and mini-cucumber as it improved biomass/architecture and first-yield, respectively. A central discovery was that dynamic 1 had a significantly higher level of photorespiration than control, for both species. Unexpectedly, photorespiration was comparable between species under the same treatments, except under constant. However, preliminary data on a fully tolerant tomato genotype grown under constant treatment upregulated photorespiration similar to mini-cucumber. These results suggest that photoperiodic injury tolerance involves a sustained higher level of photorespiration under extended photoperiods. Interestingly, diurnal MultispeQ measurements point to the importance of cyclic electron flow at subjective nighttime that may also partially explain why dynamic LED strategies mitigate photoperiodic injury. We propose an ontology of photoperiodic injury involving photorespiration, triose phosphate utilization, peroxisomal H2O2-catalase balance, and a circadian external coincidence model of sensitivity that initiates programmed cell death.

Soybean RVE8a confers salt and drought tolerance in Arabidopsis

Soybean is an economically important crop, which often suffers various abiotic stresses. REVEILLE (RVE) genes have been generally considered as circadian oscillators to mediate diverse developmental processes and plant response to environmental stresses. Addressing their roles is of significance for utilizing them to enhance agronomic traits in crops. However, our understanding of soybean RVEs is extremely limited. In the study, we investigated the expression patterns of soybean CCA1-like genes under salt stress using our RNA-Seq data. Subsequently, a salt stress-inducible gene, GmRVE8a, was chosen for further study. Phylogenetic analysis indicated that GmRVE8a is most closely related to Arabidopsis RVE4 and RVE8. Also, GmRVE8a showed circadian expression pattern with 24 h rhythmic period, suggesting that it might be a clock-regulated gene. Moreover, transgenic Arabidopsis lines over-expressing GmRVE8a were generated. It was observed that ectopic over-expression of GmRVE8a caused a significant delay in flowering. Further observation indicated that under salt and drought stress, transgenic seedlings were stronger than wild type. Consistently, three-week-old transgenic plants grew better than wild type under salt and drought conditions, and the MDA content in transgenic lines was significantly lower than wild type, suggesting that GmRVE8a might be a positive regulator in response to salt and drought stress. Intriguingly, Y2H assay indicated that GmRVE8a physically interacted with a drought-tolerant protein, GmNAC17. Overall, our findings provided preliminary information regarding the functional roles of GmRVE8a in response to salt and drought stress.

Circadian Biology and the Neurovascular Unit

Mammalian physiology and cellular function are subject to significant oscillations over the course of every 24-hour day. It is likely that these daily rhythms will affect function as well as mechanisms of disease in the central nervous system. In this review, we attempt to survey and synthesize emerging studies that investigate how circadian biology may influence the neurovascular unit. We examine how circadian clocks may operate in neural, glial, and vascular compartments, review how circadian mechanisms regulate cell-cell signaling, assess interactions with aging and vascular comorbidities, and finally ask whether and how circadian effects and disruptions in rhythms may influence the risk and progression of pathophysiology in cerebrovascular disease. Overcoming identified challenges and leveraging opportunities for future research might support the development of novel circadian-based treatments for stroke.

Integrated Metabolome and Transcriptome Analysis of Gibberellins Mediated the Circadian Rhythm of Leaf Elongation by Regulating Lignin Synthesis in Maize

Plant growth exhibits rhythmic characteristics, and gibberellins (GAs) are involved in regulating cell growth, but it is still unclear how GAs crosstalk with circadian rhythm to regulate cell elongation. The study analyzed growth characteristics of wild-type (WT), zmga3ox and zmga3ox with GA3 seedlings. We integrated metabolomes and transcriptomes to study the interaction between GAs and circadian rhythm in mediating leaf elongation. The rates of leaf growth were higher in WT than zmga3ox, and zmga3ox cell length was shorter when proliferated in darkness than light, and GA3 restored zmga3ox leaf growth. The differentially expressed genes (DEGs) between WT and zmga3ox were mainly enriched in hormone signaling and cell wall synthesis, while DEGs in zmga3ox were restored to WT by GA3. Moreover, the number of circadian DEGs that reached the peak expression in darkness was more than light, and the upregulated circadian DEGs were mainly enriched in cell wall synthesis. The differentially accumulated metabolites (DAMs) were mainly attributed to flavonoids and phenolic acid. Twenty-two DAMs showed rhythmic accumulation, especially enriched in lignin synthesis. The circadian DEGs ZmMYBr41/87 and ZmHB34/70 were identified as regulators of ZmHCT8 and ZmBM1, which were enzymes in lignin synthesis. Furthermore, GAs regulated ZmMYBr41/87 and ZmHB34/70 to modulate lignin biosynthesis for mediating leaf rhythmic growth.

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.

Time for growth

Plants measure the duration of metabolic activity to promote rapid growth in long days.

Plant biomarkers as early detection tools in stress management in food crops: a review

MAIN CONCLUSION

Plant Biomarkers are objective indicators of a plant's cellular state in response to abiotic and biotic stress factors. They can be explored in crop breeding and engineering to produce stress-tolerant crop species. Global food production safely and sustainably remains a top priority to feed the ever-growing human population, expected to reach 10 billion by 2050. However, abiotic and biotic stress factors negatively impact food production systems, causing between 70 and 100% reduction in crop yield. Understanding the plant stress responses is critical for developing novel crops that can adapt better to various adverse environmental conditions. Using plant biomarkers as measurable indicators of a plant's cellular response to external stimuli could serve as early warning signals to detect stresses before severe damage occurs. Plant biomarkers have received considerable attention in the last decade as pre-stress indicators for various economically important food crops. This review discusses some biomarkers associated with abiotic and biotic stress conditions and highlights their importance in developing stress-resilient crops. In addition, we highlighted some factors influencing the expression of biomarkers in crop plants under stress. The information presented in this review would educate plant researchers, breeders, and agronomists on the significance of plant biomarkers in stress biology research, which is essential for improving plant growth and yield toward sustainable food production.

Application of Multi-Omics Technologies to the Study of Phytochromes in Plants

Phytochromes (phy) are distributed in various plant organs, and their physiological effects influence plant germination, flowering, fruiting, and senescence, as well as regulate morphogenesis throughout the plant life cycle. Reactive oxygen species (ROS) are a key regulatory factor in plant systemic responses to environmental stimuli, with an attractive regulatory relationship with phytochromes. With the development of high-throughput sequencing technology, omics techniques have become powerful tools, and researchers have used omics techniques to facilitate the big data revolution. For an in-depth analysis of phytochrome-mediated signaling pathways, integrated multi-omics (transcriptomics, proteomics, and metabolomics) approaches may provide the answer from a global perspective. This article comprehensively elaborates on applying multi-omics techniques in studying phytochromes. We describe the current research status and future directions on transcriptome-, proteome-, and metabolome-related network components mediated by phytochromes when cells are subjected to various stimulation. We emphasize the importance of multi-omics technologies in exploring the effects of phytochromes on cells and their molecular mechanisms. Additionally, we provide methods and ideas for future crop improvement.

Mitochondrial Dynamics in Pulmonary Hypertension

Mitochondria are essential organelles for energy production, calcium homeostasis, redox signaling, and other cellular responses involved in pulmonary vascular biology and disease processes. Mitochondrial homeostasis depends on a balance in mitochondrial fusion and fission (dynamics). Mitochondrial dynamics are regulated by a viable circadian clock. Hypoxia and nicotine exposure can cause dysfunctions in mitochondrial dynamics, increases in mitochondrial reactive oxygen species generation and calcium concentration, and decreases in ATP production. These mitochondrial changes contribute significantly to pulmonary vascular oxidative stress, inflammatory responses, contractile dysfunction, pathologic remodeling, and eventually pulmonary hypertension. In this review article, therefore, we primarily summarize recent advances in basic, translational, and clinical studies of circadian roles in mitochondrial metabolism in the pulmonary vasculature. This knowledge may not only be crucial to fully understanding the development of pulmonary hypertension, but also greatly help to create new therapeutic strategies for treating this devastating disease and other related pulmonary disorders.

PSKR1 balances the plant growth-defence trade-off in the rhizosphere microbiome

Microbiota benefit their hosts by improving nutrient uptake and pathogen protection. How host immunity restricts microbiota while avoiding autoimmunity is poorly understood. Here we show that the Arabidopsis phytosulfokine receptor 1 (pskr1) mutant displays autoimmunity (plant stunting, defence-gene expression and reduced rhizosphere bacterial growth) in response to growth-promoting Pseudomonas fluorescens. Microbiome profiling and microbiota colonization showed that PSKR1-mediated reduction in bacterial growth and stunting is largely specific to Pseudomonas. Transcriptional profiling demonstrated that PSKR1 regulates the growth-defence trade-off during Pseudomonas colonization: PSKR1 upregulates plant photosynthesis and root growth but suppresses salicylic-acid-mediated defences. Genetic epistasis experiments showed that pskr1 stunting and restriction of bacterial growth are salicylic acid dependent. Finally, we showed that Pseudomonas, but not other bacteria, induces PSKR1 expression in roots, suggesting that Pseudomonas might manipulate plant signalling to promote its colonization. Our data demonstrate a genetic mechanism to coordinate beneficial functions of the microbiome while preventing autoimmunity.

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.

Circadian clock1a coordinates neutrophil recruitment via nfe212a/duox-reactive oxygen species pathway in zebrafish

Neutrophil recruitment to inflammatory sites appears to be an evolutionarily conserved strategy to fight against exogenous insults. However, the rhythmic characteristics and underlying mechanisms of neutrophil migration on a 24-h timescale are largely unknown. Using the advantage of in vivo imaging of zebrafish, this study explored how the circadian gene clock1a dynamically regulates the rhythmic recruitment of neutrophils to inflammatory challenges. We generated a clock1a mutant and found that neutrophil migration is significantly increased in caudal fin injury and lipopolysaccharide (LPS) injection. Transcriptome sequencing, chromatin immunoprecipitation (ChIP), and dual-luciferase reporting experiments suggest that the clock1a gene regulates neutrophil migration by coordinating the rhythmic expression of nfe212a and duox genes to control the reactive oxygen species (ROS) level. This study ultimately provides a visual model to expand the understanding of the rhythmic mechanisms of neutrophil recruitment on a circadian timescale in a diurnal organism from the perspective of ROS.

Transcriptional and post-translational regulation of plant autophagy

In response to changing environmental conditions, plants activate cellular responses to enable them to adapt. One such response is autophagy, in which cellular components, for example proteins and organelles, are delivered to the vacuole for degradation. Autophagy is activated by a wide range of conditions, and the regulatory pathways controlling this activation are now being elucidated. However, key aspects of how these factors may function together to properly modulate autophagy in response to specific internal or external signals are yet to be discovered. In this review we discuss mechanisms for regulation of autophagy in response to environmental stress and disruptions in cell homeostasis. These pathways include post-translational modification of proteins required for autophagy activation and progression, control of protein stability of the autophagy machinery, and transcriptional regulation, resulting in changes in transcription of genes involved in autophagy. In particular, we highlight potential connections between the roles of key regulators and explore gaps in research, the filling of which can further our understanding of the autophagy regulatory network in plants.

SlSAMS1 enhances salt tolerance through regulation DNA methylation of SlGI in tomato

S-adenosylmethionine (SAM), which is synthesized from methionine and ATP catalyzed by S-adenosylmethionine synthetase (SAMS), is an important methyl donor in plants. SAMS and DNA methylation play an important role in the plant response to abiotic stresses. Previous studies have shown that SAMS improves salt tolerance in tomato plants, but it is not clear whether the DNA methylation pathway mediates SAMS-induced salt tolerance. This study confirmed that SlSAMS1-overexpressing plants exhibited improved salt tolerance. Through whole-genome bisulfite sequencing (WGBS) and transcriptome sequencing (RNA-seq) analysis, the study screened the circadian rhythm pathway and identified the gene SlGI in this pathway, which was regulated by SlSAMS1. The gene body region of SlGI, the core gene of the circadian rhythm pathway, was hypermethylated in SlSAMS1-overexpressing plants, and its expression level was significantly increased. Furthermore, the SlGI-overexpressing plants showed higher salt tolerance, less reduction in plant height and fresh weight, lower electrolyte leakage, malondialdehyde and H2O2 content, and higher antioxidant enzyme activity compared to wild type plants. Therefore, SlSAMS1-overexpressing plants regulated significant changes in CHG-type methylation sites of the SlGI gene body and its expression levels, leading to an enhanced salt tolerance of tomato plants.

Environmental and behavioral regulation of HIF-mitochondria crosstalk

Reduced oxygen availability (hypoxia) can lead to cell and organ damage. Therefore, aerobic species depend on efficient mechanisms to counteract detrimental consequences of hypoxia. Hypoxia inducible factors (HIFs) and mitochondria are integral components of the cellular response to hypoxia and coordinate both distinct and highly intertwined adaptations. This leads to reduced dependence on oxygen, improved oxygen supply, maintained energy provision by metabolic remodeling and tapping into alternative pathways and increased resilience to hypoxic injuries. On one hand, many pathologies are associated with hypoxia and hypoxia can drive disease progression, for example in many cancer and neurological diseases. But on the other hand, controlled induction of hypoxia responses via HIFs and mitochondria can elicit profound health benefits and increase resilience. To tackle pathological hypoxia conditions or to apply health-promoting hypoxia exposures efficiently, cellular and systemic responses to hypoxia need to be well understood. Here we first summarize the well-established link between HIFs and mitochondria in orchestrating hypoxia-induced adaptations and then outline major environmental and behavioral modulators of their interaction that remain poorly understood.

The Chemical Composition and Transcriptome Analysis Reveal the Mechanism of Color Formation in Tea (Camellia sinensis) Pericarp

To elucidate the molecular mechanisms underlying the differential metabolism of albino (white), green, and purple pericarp coloration, biochemical profiling and transcriptome sequencing analyses were performed on three different tea pericarps, Zhongbaiyihao (Camellia sinensis L. var. Zhongbai), Jinxuan (Camellia sinensis L. var. Jinxuan), and Baitangziya (Camellia sinensis L. var. Baitang). Results of biochemical analysis revealed that low chlorophyll content and low chlorophyll/carotene ratio may be the biochemical basis for albino characteristics in the 'Zhongbaiyihao' pericarp. The differentially expressed genes (DEGs) involved in anthocyanin biosynthesis, including DFR, F3'5'H, CCoAOMT, and 4-coumaroyl-CoA, were highly expressed in the purple 'Baitangziya' pericarp. In the chlorophyll synthesis of white pericarp, GUN5 (Genome Uncoupled 5) and 8-vinyl-reductase both showed high expression levels compared to the green one, which indicated that albino 'Zhongbaiyihao' pericarp had a higher chlorophyll synthesis capacity than 'Jinxuan'. Meanwhile, chlorophyllase (CLH, CSS0004684) was lower in 'Baitang' than in 'Jinxuan' and 'Zhongbaiyihao' pericarp. Among the differentially expressed transcription factors, MYB59, WRKY41-like2 (CS ng17509), bHLH62 like1 (CS ng6804), and bHLH62-like3 (CSS0039948) were downregulated in Jinxuan pericarp, suggesting that transcription factors played a role in regulating tea pericarp coloration. These findings provide a better understanding of the molecular mechanisms and theoretical basis for utilizing functional components of tea pericarp.

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.

Late Elongated Hypocotyl Positively Regulates Salt Stress Tolerance in Medicago truncatula

Abiotic stress, such as drought, osmotic, and salinity stresses, seriously affects plant growth and crop production. Studying stress-resistant genes that enhance plant stress tolerance is an efficient way to facilitate the breeding of crop species with high stress tolerance. In this study, we reported that the core circadian clock component, the LATE ELONGATED HYPOCOTYL (LHY) orthologue MtLHY, plays a positive role in salt stress response in Medicago truncatula. The expression of MtLHY was induced by salt stress, and loss-of-function mutants of MtLHY were shown to be hypersensitive to salt treatment. However, overexpression of MtLHY improved salt stress tolerance through a higher accumulation of flavonoids. Consistently, exogenous flavonol application improved the salt stress tolerance in M. truncatula. Additionally, MtLHY was identified as a transcriptional activator of the flavonol synthase gene, MtFLS. Our findings revealed that MtLHY confers plant salt stress tolerance, at least by modulating the flavonoid biosynthesis pathway, which provides insight into salt stress tolerance that links the circadian clock with flavonoid biosynthesis.

A bittersweet symphony: Metabolic signals in the circadian system

Plants must match their metabolism to daily and seasonal fluctuations in their environment to maximise performance in natural conditions. Circadian clocks enable organisms to anticipate and adapt to these predictable and unpredictable environmental challenges. Metabolism is increasingly recognised as an integrated feature of the plant circadian system. Metabolism is an important circadian-regulated output but also provides input to this dynamic timekeeping mechanism. The spatial organisation of metabolism within cells and between tissues, and the temporal features of metabolism across days, seasons and development, raise interesting questions about how metabolism influences circadian timekeeping. The various mechanisms by which metabolic signals influence the transcription-translation feedback loops of the circadian oscillator are emerging. These include roles for major metabolic signalling pathways, various retrograde signals, and direct metabolic modifications of clock genes or proteins. Such metabolic feedback loops enable intra- and intercellular coordination of rhythmic metabolism, and recent discoveries indicate these contribute to diverse aspects of daily, developmental and seasonal timekeeping.

Submergence Stress Alters the Expression of Clock Genes and Configures New Zeniths and Expression of Outputs in Brachypodium distachyon

Plant networks of oscillating genes coordinate internal processes with external cues, contributing to increased fitness. We hypothesized that the response to submergence stress may dynamically change during different times of the day. In this work, we determined the transcriptome (RNA sequencing) of the model monocotyledonous plant, Brachypodium distachyon, during a day of submergence stress, low light, and normal growth. Two ecotypes of differential tolerance, Bd21 (sensitive) and Bd21-3 (tolerant), were included. We submerged 15-day-old plants under a long-day diurnal cycle (16 h light/8 h dark) and collected samples after 8 h of submergence at ZT0 (dawn), ZT8 (midday), ZT16 (dusk), ZT20 (midnight), and ZT24 (dawn). Rhythmic processes were enriched both with up- and down-regulated genes, and clustering highlighted that the morning and daytime oscillator components (PRRs) show peak expression in the night, and a decrease in the amplitude of the clock genes (GI, LHY, RVE) was observed. Outputs included photosynthesis-related genes losing their known rhythmic expression. Up-regulated genes included oscillating suppressors of growth, hormone-related genes with new late zeniths (e.g., JAZ1, ZEP), and mitochondrial and carbohydrate signaling genes with shifted zeniths. The results highlighted genes up-regulated in the tolerant ecotype such as METALLOTHIONEIN3 and ATPase INHIBITOR FACTOR. Finally, we show by luciferase assays that Arabidopsis thaliana clock genes are also altered by submergence changing their amplitude and phase. This study can guide the research of chronocultural strategies and diurnal-associated tolerance mechanisms.

The Regulatory Networks of the Circadian Clock Involved in Plant Adaptation and Crop Yield

Global climatic change increasingly threatens plant adaptation and crop yields. By synchronizing internal biological processes, including photosynthesis, metabolism, and responses to biotic and abiotic stress, with external environmental cures, such as light and temperature, the circadian clock benefits plant adaptation and crop yield. In this review, we focus on the multiple levels of interaction between the plant circadian clock and environmental factors, and we summarize recent progresses on how the circadian clock affects yield. In addition, we propose potential strategies for better utilizing the current knowledge of circadian biology in crop production in the future.

The MYB59 transcription factor negatively regulates salicylic acid- and jasmonic acid-mediated leaf senescence

Leaf senescence is the final stage of leaf development and is affected by various exogenous and endogenous factors. Transcriptional regulation is essential for leaf senescence, however, the underlying molecular mechanisms remain largely unclear. In this study, we report that the transcription factor MYB59, which was predominantly expressed in early senescent rosette leaves, negatively regulates leaf senescence in Arabidopsis (Arabidopsis thaliana). RNA sequencing revealed a large number of differentially expressed genes involved in several senescence-related biological processes in myb59-1 rosette leaves. Chromatin immunoprecipitation and transient dual-luciferase reporter assays demonstrated that MYB59 directly repressed the expression of SENESCENCE ASSOCIATED GENE 18 and indirectly inhibited the expression of several other senescence-associated genes to delay leaf senescence. Moreover, MYB59 was induced by salicylic acid (SA) and jasmonic acid (JA). MYB59 inhibited SA production by directly repressing the expression of ISOCHORISMATE SYNTHASE 1 and PHENYLALANINE AMMONIA-LYASE 2 and restrained JA biosynthesis by directly suppressing the expression of LIPOXYGENASE 2, thus forming two negative feedback regulatory loops with SA and JA and ultimately delaying leaf senescence. These results help us understand the novel function of MYB59 and provide insights into the regulatory network controlling leaf senescence in Arabidopsis.

Mutation of Arabidopsis SME1 and Sm core assembly improves oxidative stress resilience

Alternative splicing is a key posttranscriptional gene regulatory process, acting in diverse adaptive and basal plant processes. Splicing of precursor-messenger RNA (pre-mRNA) is catalyzed by a dynamic ribonucleoprotein complex, designated the spliceosome. In a suppressor screen, we identified a nonsense mutation in the Smith (Sm) antigen protein SME1 to alleviate photorespiratory H₂O₂-dependent cell death in catalase deficient plants. Similar attenuation of cell death was observed upon chemical inhibition of the spliceosome, suggesting pre-mRNA splicing inhibition to be responsible for the observed cell death alleviation. Furthermore, the sme1-2 mutants showed increased tolerance to the reactive oxygen species inducing herbicide methyl viologen. Both an mRNA-seq and shotgun proteomic analysis in sme1-2 mutants displayed a constitutive molecular stress response, together with extensive alterations in pre-mRNA splicing of transcripts encoding metabolic enzymes and RNA binding proteins, even under unstressed conditions. Using SME1 as a bait to identify protein interactors, we provide experimental evidence for almost 50 homologs of the mammalian spliceosome-associated protein to reside in the Arabidopsis thaliana spliceosome complexes and propose roles in pre-mRNA splicing for four uncharacterized plant proteins. Furthermore, as for sme1-2, a mutant in the Sm core assembly protein ICLN resulted in a decreased sensitivity to methyl viologen. Taken together, these data show that both a perturbed Sm core composition and assembly results in the activation of a defense response and in enhanced resilience to oxidative stress.

Regulatory Effects of Clock and Bmal1 on Circadian Rhythmic TLR Expression

Circadian locomotor output cycles kaput (Clock) and brain and muscle ARNT-like 1 (Bmal1) are two core circadian clock genes. They form a heterodimer that can bind to the E-box element in the promoters of Period circadian protein (Per) and Cryptochrome (Cry) genes, thereby inducing the rhythmic expression of circadian clock control genes. Toll-like receptors (TLRs) are type I transmembrane proteins belonging to the pattern recognition receptor (PRR) family. They can recognize a variety of pathogens and play an important role in innate immunity and adaptive immune responses. Recent studies have found that the circadian clock is closely associated with the immune system. TLRs have a certain correlation with the circadian rhythms; Bmal1 seems to be the central mediator connecting the circadian clock and the immune system. Research on Bmal1 and TLRs has made some progress, but the specific relationship between TLRs and Bmal1 remains unclear. Understanding the relationship between TLRs and Clock/Bmal1 genes is increasingly important for basic research and clinical treatment.

Existence of circadian rhythm and its response behavior under different storage conditions of soybean sprouts

The circadian system plays an essential role in plant cells, and numerous physiological events are generally modulated by circadian clock genes. To further improve postharvest handling of fresh produce, it is vital to understanding the behavior of clock gene expression and its underlying interactions with changes in quality. In this study, the effect of temperature and controlled atmosphere storage on the expression of clock genes (GmLCL1, GmPRR7, GmGI, GmTOC1, and GmLUX), postharvest quality characteristics and their related genes in soybean sprouts were investigated. By fitting the obtained gene expression level using the qPCR method with the cosine curve equation, it was successfully found that the circadian rhythm existed under constant dark storage conditions of soybean sprouts. A significant rhythm in clock gene expression was observed in control soybean sprouts. In contrast, low temperature storage diminished the cyclic expression of GmLCL1, GmPRR7, and GmTOC1, which also affected GmGI and GmLUX expression. Additionally, high CO₂ concentrations during storage disturbed the circadian clock by affecting the phase and amplitude of each gene; for low O₂ concentrations, it was only affected by amplitude. Interestingly, low temperature, low O₂, and high CO₂ maintained postharvest quality, including reduced respiration, weight loss and browning incidence. The expression behaviors of postharvest quality attribute-related genes (GmFUM1, GmCS, Gm2-OGDH, GmPPO1, GmPAL) were also influenced by the storage treatments. Overall, the findings first suggest a possible link between clock disruption and postharvest quality maintenance of soybean sprouts.

Changing winter climate and snow conditions induce various transcriptional stress responses in Scots pine seedlings

In northern boreal forests the warming winter climate leads to more frequent snowmelt, rain-on-snow events and freeze-thaw cycles. This may be harmful or even lethal for tree seedlings that spend even a half of the year under snow. We conducted a snow cover manipulation experiment in a natural forest to find out how changing snow conditions affect young Scots pine (Pinus sylvestris L.) seedlings. The ice encasement (IE), absence of snow (NoSNOW) and snow compaction (COMP) treatments affected ground level temperature, ground frost and subnivean gas concentrations compared to the ambient snow cover (AMB) and led to the increased physical damage and mortality of seedlings. The expression responses of 28 genes related to circadian clock, aerobic and anaerobic energy metabolism, carbohydrate metabolism and stress protection revealed that seedlings were exposed to different stresses in a complex way depending on the thickness and quality of the snow cover. The IE treatment caused hypoxic stress and probably affected roots which resulted in reduced water uptake in the beginning of the growing season. Without protective snowpack in NoSNOW seedlings suffered from cold and drought stresses. The combination of hypoxic and cold stresses in COMP evoked unique transcriptional responses including oxidative stress. Snow cover manipulation induced changes in the expression of several circadian clock related genes suggested that photoreceptors and the circadian clock system play an essential role in the adaptation of Scots pine seedlings to stresses under different snow conditions. Our findings show that warming winter climate alters snow conditions and consequently causes Scots pine seedlings various abiotic stresses, whose effects extend from overwintering to the following growing season.

Phytochromes and Their Role in Diurnal Variations of ROS Metabolism and Plant Proteome

Plants are sessile organisms forced to adapt to environmental variations recurring in a day-night cycle. Extensive research has uncovered the transcriptional control of plants' inner clock and has revealed at least some part of the intricate and elaborate regulatory mechanisms that govern plant diel responses and provide adaptation to the ever-changing environment. Here, we analyzed the proteome of the Arabidopsis thaliana mutant genotypes collected in the middle of the day and the middle of the night, including four mutants in the phytochrome (phyA, phyB, phyC, and phyD) and the circadian clock protein LHY. Our approach provided a novel insight into the diel regulations, identifying 640 significant changes in the night-day protein abundance. The comparison with previous studies confirmed that a large portion of identified proteins was a known target of diurnal regulation. However, more than 300 were novel oscillations hidden under standard growth chamber conditions or not manifested in the wild type. Our results indicated a prominent role for ROS metabolism and phytohormone cytokinin in the observed regulations, and the consecutive analyses confirmed that. The cytokinin signaling significantly increased at night, and in the mutants, the hydrogen peroxide content was lower, and the night-day variation seemed to be lost in the phyD genotype. Furthermore, regulations in the lhy and phyB mutants were partially similar to those found in the catalase mutant cat2, indicating shared ROS-mediated signaling pathways. Our data also shed light on the role of the relatively poorly characterized Phytochrome D, pointing to its connection to glutathione metabolism and the regulation of glutathione S-transferases.

The circadian night depression of photosynthesis analyzed in a herb, Pulmonaria vallarsae. Day/night quantitative relationships

Although many photosynthesis related processes are known to be controlled by the circadian system, consequent changes in photosynthetic activities are poorly understood. Photosynthesis was investigated during the daily cycle by chlorophyll fluorescence using a PAM fluorometer in Pulmonaria vallarsae subsp. apennina, an understory herb. A standard test consists of a light induction pretreatment followed by light response curve (LRC). Comparison of the major diagnostic parameters collected during day and night showed a nocturnal drop of photosynthetic responses, more evident in water-limited plants and consisting of: (i) strong reduction of flash-induced fluorescence peaks (FIP), maximum linear electron transport rate (Jmax, ETR_EM) and effective PSII quantum yield (Φ_PSII); (ii) strong enhancement of nonphotochemical quenching (NPQ) and (iii) little or no change in photochemical quenching qP, maximum quantum yield of linear electron transport (Φ), and shape of LRC (θ). A remarkable feature of day/night LRCs at moderate to high irradiance was their linear-parallel course in double-reciprocal plots. Photosynthesis was also monitored in plants subjected to 2-3 days of continuous darkness ("long night"). In such conditions, plants exhibited high but declining peaks of photosynthetic activity during subjective days and a low, constant value with elevated NPQ during subjective night tests. The photosynthetic parameters recorded in subjective days in artificial darkness resembled those under natural day conditions. On the basis of the evidence, we suggest a circadian component and a biochemical feedback inhibition to explain the night depression of photosynthesis in P. vallarsae.

Two central circadian oscillators OsPRR59 and OsPRR95 modulate magnesium homeostasis and carbon fixation in rice

Photosynthesis, which provides oxygen and energy for all living organisms, is circadian regulated. Photosynthesis-associated metabolism must tightly coordinate with the circadian clock to maximize the efficiency of the light-energy capture and carbon fixation. However, the molecular basis for the interplay of photosynthesis and the circadian clock is not fully understood, particularly in crop plants. Here, we report two central oscillator genes of circadian clock, OsPRR95 and OsPRR59 in rice, which function as transcriptional repressors to negatively regulate the rhythmic expression of OsMGT3 encoding a chloroplast-localized Mg²⁺ transporter. OsMGT3-dependent rhythmic Mg fluctuations modulate carbon fixation and consequent sugar output in rice chloroplasts. Furthermore, sugar triggers the increase of superoxide, which may act as a feedback signal to positively regulate the expression of OsPRR95 and OsPRR59. Taken together, our results reveal a negative-feedback loop that strengthens the crosstalk between photosynthetic carbon fixation and the circadian clock, which may improve plan adaptation and performance in fluctuating environments.

Circadian Redox Rhythm in Plant-Fungal Pathogen Interactions

Significance: Circadian-controlled cellular growth, differentiation, and metabolism are mainly achieved by a classical transcriptional-translational feedback loop (TTFL), as revealed by investigations in animals, plants, and fungi. Recent Advances: Recently, reactive oxygen species (ROS) have been reported as part of a cellular network synchronizing nontranscriptional oscillators with established TTFL components, adding complexity to regulatory mechanisms of circadian rhythm. Both circadian rhythm and ROS homeostasis have a great impact on plant immunity as well as fungal pathogenicity, therefore interconnections of these two factors are implicit in plant-fungus interactions. Critical Issues: In this review, we aim to summarize the recent advances in circadian-controlled ROS homeostasis, or ROS-modulated circadian clock, in plant-fungus pathosystems, particularly using the rice (Oryza sativa) blast fungus (Magnaporthe oryzae) pathosystem as an example. Understanding of such bidirectional interaction between the circadian timekeeping machinery and ROS homeostasis/signaling would provide a theoretical basis for developing disease control strategies for important plants/crops. Future Directions: Questions remain unanswered about the detailed mechanisms underlying circadian regulation of redox homeostasis in M. oryzae, and the consequent fungal differentiation and death in a time-of-day manner. We believe that the rice-M. oryzae pathobiosystem would provide an excellent platform for investigating such issues in circadian-ROS interconnections in a plant-fungus interaction context. Antioxid. Redox Signal. 37, 726-738.

Dark secrets of phytomelatonin

Phytomelatonin is a newly identified plant hormone, and its primary functions in plant growth and development remain relatively poorly appraised. Phytomelatonin is a master regulator of reactive oxygen species (ROS) signaling and acts as a darkness signal in circadian stomatal closure. Plants exhibit at least three interrelated patterns of interaction between phytomelatonin and ROS production. Exogenous melatonin can induce flavonoid biosynthesis, which might be required for maintenance of antioxidant capacity under stress, after harvest, and in leaf senescence conditions. However, several genetic studies have provided direct evidence that phytomelatonin plays a negative role in the biosynthesis of flavonoids under non-stress conditions. Phytomelatonin delays flowering time in both dicot and monocot plants, probably via its receptor PMTR1 and interactions with the gibberellin, strigolactone, and ROS signaling pathways. Furthermore, phytomelatonin signaling also functions in hypocotyl and shoot growth in skotomorphogenesis and ultraviolet B (UV-B) exposure; the G protein α-subunit (Arabidopsis GPA1 and rice RGA1) and constitutive photomorphogenic1 (COP1) are important signal components during this process. Taken together, these findings indicate that phytomelatonin acts as a darkness signal with important regulatory roles in circadian stomatal closure, flavonoid biosynthesis, flowering, and hypocotyl and shoot growth.

Molecular mechanisms and evolutionary history of phytomelatonin in flowering

Flowering is a critical stage in plant life history, which is coordinated by environmental signals and endogenous cues. Phytomelatonin is a widely distributed indoleamine present in all living organisms and plays pleiotropic roles in plant growth and development. Recent evidence has established that phytomelatonin could modulate flowering in many species, probably in a concentration-dependent manner. Phytomelatonin seems to associate with floral meristem identification and floral organ formation, and the fluctuation of phytomelatonin might be important for flowering. Regarding the underlying mechanisms, phytomelatonin interacts with the central components of floral gene regulatory networks directly or indirectly, including the MADS-box gene family, phytohormones, and reactive oxygen species (ROS). From an evolutionary point of view, the actions of phytomelatonin in flowering probably evolved during the period of the diversification of flowering plants and could be regarded as a functional extension of its primary activities. The presumed evolutionary history of phytomelatonin-modulated flowering is proposed, presented in the chronological order of the appearance of phytomelatonin and core flowering regulators, namely DELLA proteins, ROS, and phytohormones. Further efforts are needed to address some intriguing aspects, such as the exploration of the association between phytomelatonin and photoperiodic flowering, phytomelatonin-related floral MADS-box genes, the crosstalk between phytomelatonin and phytohormones, as well as its potential applications in agriculture.