Chlorophyll breakdown in senescent Arabidopsis leaves. Characterization of chlorophyll catabolites and of chlorophyll catabolic enzymes involved in the degreening reaction

Improved pokeweed genome assembly and early gene expression changes in response to jasmonic acid

BACKGROUND

Jasmonic acid (JA) is a phytohormone involved in regulating responses to biotic and abiotic stress. Although the JA pathway is well characterized in model plants such as Arabidopsis thaliana, less is known about many non-model plants. Phytolacca americana (pokeweed) is native to eastern North Americana and is resilient to environmental stress. The goal of this study was to produce a publicly available pokeweed genome assembly and annotations and use this resource to determine how early response to JA changes gene expression, with particular focus on genes involved in defense.

RESULTS

We assembled the pokeweed genome de novo from approximately 30 Gb of PacBio Hifi long reads and achieved an NG50 of ~ 13.2 Mb and a minimum 93.9% complete BUSCO score for gene annotations. With this reference, we investigated the early changes in pokeweed gene expression following JA treatment. Approximately 5,100 genes were differentially expressed during the 0-6 h time course with almost equal number of genes with increased and decreased transcript levels. Cluster and gene ontology analyses indicated the downregulation of genes associated with photosynthesis and upregulation of genes involved in hormone signaling and defense. We identified orthologues of key transcription factors and constructed the first JA gene response network integrated with our transcriptomic data from orthologues of Arabidopsis genes. We discovered that pokeweed did not use leaf senescence as a means of reallocating resources during stress; rather, most secondary metabolite synthesis genes were constitutively expressed, suggesting that pokeweed directs its resources for survival over the long term. In addition, pokeweed synthesizes several RNA N-glycosylases hypothesized to function in defense, each with unique expression profiles in response to JA.

CONCLUSIONS

Our investigation of the early response of pokeweed to JA illustrates patterns of gene expression involved in defence and stress tolerance. Pokeweed provides insight into the defense mechanisms of plants beyond those observed in research models and crops, and further study may yield novel approaches to improving the resilience of plants to environmental changes. Our assembled pokeweed genome is the first within the taxonomic family Phytolaccaceae to be publicly available for continued research.

Reactive oxygen species act as the key signaling molecules mediating light-induced anthocyanin biosynthesis in Eucalyptus

Light plays a pivotal role in regulating anthocyanin biosynthesis in plants, and the early light-responsive signals that initiate anthocyanin biosynthesis remain to be elucidated. In this study, we showed that the anthocyanin biosynthesis in Eucalyptus is hypersensitive to increased light intensity. The combined transcriptomic and metabolomic analyses were conducted on Eucalyptus leaves after moderate (ML; 100 μmol m-2 s-1) and high (HL; 300 μmol m-2 s-1) light intensity treatments. The results identified 1940, 1096, 1173, and 2756 differentially expressed genes at 6, 12, 24, and 36 h after HL treatment, respectively. The metabolomic results revealed the primary anthocyanin types, and other differentially accumulated flavonoids and phenylpropane intermediates that were produced in response to HL, which well aligned with the transcriptome results. Moreover, biochemical analysis showed that HL inhibited peroxidase activity and increased the ROS level in Eucalyptus leaves. ROS depletion through co-application of the antioxidants rutin, uric acid, and melatonin significantly reduced, and even abolished, anthocyanin biosynthesis induced by HL treatment. Additionally, exogenous application of hydrogen peroxide efficiently induced anthocyanin biosynthesis within 24 h, even under ML conditions, suggesting that ROS played a major role in activating anthocyanin biosynthesis. A HL-responsive MYB transcription factor EgrMYB113 was identified to play an important role in regulating anthocyanin biosynthesis by targeting multiple anthocyanin biosynthesis genes. Additionally, the results demonstrated that gibberellic acid and sugar signaling contributed to HL-induced anthocyanin biosynthesis. Conclusively, these results suggested that HL triggers multiple signaling pathways to induce anthocyanin biosynthesis, with ROS acting as indispensable mediators in Eucalyptus.

Novel Types of Phyllobilins in a Fern - Molecular Reporters of the Evolution of Chlorophyll Breakdown in the Paleozoic Era

Breakdown of chlorophyll (Chl), as studied in angiosperms, follows the pheophorbide a oxygenase/phyllobilin (PaO/PB) pathway, furnishing linear tetrapyrroles, named phyllobilins (PBs). In an investigation with fern leaves we have discovered iso-phyllobilanones (iPBs) with an intriguingly rearranged and oxidized carbon skeleton. We report here a key second group of iPBs from the fern and on their structure analysis. Previously, these additional Chl-catabolites escaped their characterization, since they exist in aqueous media as mixtures of equilibrating isomers. However, their chemical dehydration furnished stable iPB-derivatives that allowed the delineation of the enigmatic structures and chemistry of the original natural catabolites. The structures of all fern-iPBs reflect the early core steps of a PaO/PB-type pathway and the PB-to-iPB carbon skeleton rearrangement. A striking further degradative chemical ring-cleavage was observed, proposed to consume singlet molecular oxygen (1O2). Hence, Chl-catabolites may play a novel active role in detoxifying cellular 1O2. The critical deviations from the PaO/PB pathway, found in the fern, reflect evolutionary developments of Chl-breakdown in the green plants in the Paleozoic era.

Comparative genomics analysis of pheophorbide a oxygenase (PAO) genes in eight pyrus genomes and their regulatory role in multiple stress responses in Chinese pear (Pyrus bretschneideri)

Pyrus (pear) is among the most nutritious fruits and contains fibers that have great health benefits to humans. It is mostly cultivated in temperate regions globally and is highly subjected to biotic and abiotic stresses which affect its yield. Pheophorbide a oxygenase (PAO) is an essential component of the chlorophyll degradation system and contributes to the senescence of leaves. It is responsible for opening the pheophorbide a porphyrin macrocycle and forming the main fluorescent chlorophyll catabolite However, this gene family and its members have not been explored in Pyrus genomes. Here we report a pangenome-wide investigation has been conducted on eight Pyrus genomes: Cuiguan, Shanxi Duli, Zhongai 1, Nijisseiki, Yunhong No.1, d'Anjou, Bartlett v2.0, and Dangshansuli v.1.1. The phylogenetic history, their gene structure, conservation patterns of motifs, their distribution on chromosomes, and gene duplication are studied in detail which shows the intraspecific structural conservation as well as evolutionary patterns of Pyrus PAOs. Cis-elements, protein-protein interactions (PPI), and the Gene Ontology (GO) enrichment analyses show their potential biological functions. Furthermore, their expression in various tissues, fruit hardening conditions, and drought stress conditions is also studied. Based on phylogenetics, the identified PAOs were divided into four groups. The expansion of this gene family in Pyrus is caused by both tandem and segmental duplication. Moreover, positive and negative selection pressure equally directed the gene's duplication process. The Pyrus PAO genes were enriched in hormones-related, light, development, and stress-related elements. RNA-seq data analysis showed that PAOs have varied levels of expression under diseased and abiotic stress conditions. The 3D structures of PAOs are also predicted to get more insights into functional conservation. Our research can be used further to get a deeper knowledge of the PAO gene family in Pyrus and to guide future research on improving the genetic composition of Pyrus to enhance stress tolerance.

Cytokinin promotes anthocyanin biosynthesis via regulating sugar accumulation and MYB113 expression in Eucalyptus

Anthocyanins are flavonoid-like substances that play important roles in plants' adaptation to various environmental stresses. In this research, we discovered that cytokinin (CK) alone could effectively induce the anthocyanin biosynthesis in Eucalyptus and many other perennial woody plant species, but not in tobacco and Arabidopsis, suggesting a diverse role of CK in regulating anthocyanin biosynthesis in different species. Transcriptomic and metabolomic strategies were used to further clarify the specific role of CK in regulating anthocyanin biosynthesis in Eucalyptus. The results showed that 801 and 2241 genes were differentially regulated at 6 and 24 h, respectively, after CK treatment. Pathway analysis showed that most of the differentially expressed genes were categorized into pathways related to cellular metabolism or transport of metabolites, including amino acids and sugars. The metabolomic results well supported the transcriptome data, which showed that most of the differentially regulated metabolites were related to the metabolism of sugar, amino acids and flavonoids. Moreover, CK treatment significantly induced the accumulation of sucrose in the CK-treated leaves, while sugar starvation mimicked by either defoliation or shading treatment of the basal leaves significantly reduced the sugar increase of the CK-treated leaves and thus inhibited CK-induced anthocyanin biosynthesis. The results of in vitro experiment also suggested that CK-induced anthocyanin in Eucalyptus was sugar-dependent. Furthermore, we identified an early CK-responsive transcription factor MYB113 in Eucalyptus, the expression of which was significantly upregulated by CK treatment in Eucalyptus, but was inhibited in Arabidopsis. Importantly, the overexpression of EgrMYB113 in the Eucalyptus hairy roots was associated with significant anthocyanin accumulation and upregulation of most of the anthocyanin biosynthetic genes. In conclusion, our study demonstrates a key role of CK in the regulation of anthocyanin biosynthesis in Eucalyptus, providing a molecular basis for further understanding the regulatory mechanism and diversity of hormone-regulated anthocyanin biosynthesis in different plant species.

Non-coding RNAs and leaf senescence: Small molecules with important roles

Non-coding RNAs (ncRNAs) are a special class of functional RNA molecules that are not translated into proteins. ncRNAs have emerged as pivotal regulators of diverse developmental processes in plants. Recent investigations have revealed the association of ncRNAs with the regulation of leaf senescence, a complex and tightly regulated developmental process. However, a comprehensive review of the involvement of ncRNAs in the regulation of leaf senescence is still lacking. This manuscript aims to summarize the molecular mechanisms underlying ncRNAs-mediated leaf senescence and the potential applications of ncRNAs to manipulate the onset and progression of leaf senescence. Various classes of ncRNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), are discussed in terms of their regulatory mechanisms in leaf senescence. Furthermore, we explore the interactions between ncRNA and the key regulators of senescence, including transcription factors as well as core components in phytohormone signaling pathways. We also discuss the possible challenges and approaches related to ncRNA-mediated leaf senescence. This review contributes to a further understanding of the intricate regulatory network involving ncRNAs in leaf senescence.

Rice Basic Helix-Loop-Helix 079 (OsbHLH079) Delays Leaf Senescence by Attenuating ABA Signaling

Leaf senescence represents the final phase of leaf development and is characterized by a highly organized degenerative process involving the active translocation of nutrients from senescing leaves to growing tissues or storage organs. To date, a large number of senescence-associated transcription factors (sen-TFs) have been identified that regulate the initiation and progression of leaf senescence. Many of these TFs, including NAC (NAM/ATAF1/2/CUC2), WRKY, and MYB TFs, have been implicated in modulating the expression of downstream senescence-associated genes (SAGs) and chlorophyll degradation genes (CDGs) under the control of phytohormones. However, the involvement of basic helix-loop-helix (bHLH) TFs in leaf senescence has been less investigated. Here, we show that OsbHLH079 delays both natural senescence and dark-induced senescence: Overexpression of OsbHLH079 led to a stay-green phenotype, whereas osbhlh079 knockout mutation displayed accelerated leaf senescence. Similar to other sen-TFs, OsbHLH079 showed a gradual escalation in expression as leaves underwent senescence. During this process, the mRNA levels of SAGs and CDGs remained relatively low in OsbHLH079 overexpressors, but increased sharply in osbhlh079 mutants, suggesting that OsbHLH079 negatively regulates the transcription of SAGs and CDGs under senescence conditions. Additionally, we found that OsbHLH079 delays ABA-induced senescence. Subsequent RT-qPCR and dual-luciferase reporter assays revealed that OsbHLH079 downregulates the expression of ABA signaling genes, such as OsABF2, OsABF4, OsABI5, and OsNAP. Taken together, these results demonstrate that OsbHLH079 functions in delaying leaf yellowing by attenuating the ABA responses.

STAY-GREEN Accelerates Chlorophyll Degradation in Magnolia sinostellata under the Condition of Light Deficiency

Species of the Magnoliaceae family are valued for their ornamental qualities and are widely used in landscaping worldwide. However, many of these species are endangered in their natural environments, often due to being overshadowed by overstory canopies. The molecular mechanisms of Magnolia's sensitivity to shade have remained hitherto obscure. Our study sheds light on this conundrum by identifying critical genes involved in governing the plant's response to a light deficiency (LD) environment. In response to LD stress, Magnolia sinostellata leaves were endowed with a drastic dwindling in chlorophyll content, which was concomitant to the downregulation of the chlorophyll biosynthesis pathway and upregulation in the chlorophyll degradation pathway. The STAY-GREEN (MsSGR) gene was one of the most up-regulated genes, which was specifically localized in chloroplasts, and its overexpression in Arabidopsis and tobacco accelerated chlorophyll degradation. Sequence analysis of the MsSGR promoter revealed that it contains multiple phytohormone-responsive and light-responsive cis-acting elements and was activated by LD stress. A yeast two-hybrid analysis resulted in the identification of 24 proteins that putatively interact with MsSGR, among which eight were chloroplast-localized proteins that were significantly responsive to LD. Our findings demonstrate that light deficiency increases the expression of MsSGR, which in turn regulates chlorophyll degradation and interacts with multiple proteins to form a molecular cascade. Overall, our work has uncovered the mechanism by which MsSGR mediates chlorophyll degradation under LD stress conditions, providing insight into the molecular interactions network of MsSGR and contributing to a theoretical framework for understanding the endangerment of wild Magnoliaceae species.

Phyllobilins - Bioactive Natural Products Derived from Chlorophyll - Plant Origins, Structures, Absorption Spectra, and Biomedical Properties

Phyllobilins are open-chain products of the biological degradation of chlorophyll a in higher plants. Recent studies reveal that phyllobilins exert anti-oxidative and anti-inflammatory properties, as well as activities against cancer cells, that contribute to the human health benefits of numerous plants. In general, phyllobilins have been overlooked in phytochemical analyses, and - more importantly - in the analyses of medicinal plant extracts. Nevertheless, over the past three decades, > 70 phyllobilins have been identified upon examination of more than 30 plant species. Eight distinct chromophoric classes of phyllobilins are known: phyllolumibilins (PluBs), phylloleucobilins (PleBs), phylloxanthobilins (PxBs), and phylloroseobilins (PrBs)-each in type-I or type-II groups. Here, we present a database of absorption and fluorescence spectra that has been compiled of 73 phyllobilins to facilitate identification in phytochemical analyses. The spectra are provided in digital form and can be viewed and downloaded at www.photochemcad.com. The present review describes the plant origin, molecular structure, and absorption and fluorescence features of the 73 phyllobilins, along with an overview of key medicinal properties. The review should provide an enabling tool for the community for the straightforward identification of phyllobilins in plant extracts, and the foundation for deeper understanding of these ubiquitous but underexamined plant-derived micronutrients for human health.

Potential Role of Biochar and Silicon in Improving Physio-Biochemical and Yield Characteristics of Borage Plants under Different Irrigation Regimes

Silicon (Si) and biochar (Bc) are key signaling conditioners that improve plant metabolic processes and promote drought tolerance. However, the specific role of their integrative application under water restrictions on economical plants is not yet well understood. Two field experiments throughout 2018/2019 and 2019/2020 were conducted to examine the physio-biochemical modifications and yield attributes of borage plants mediated by Bc (9.52 tons ha^-1) and/or Si (300 mg L^-1) under different irrigation regimes (100, 75, and 50% of crop evapotranspiration). Catalase (CAT) and peroxidase (POD) activity; relative water content, water, and osmotic potential; leaf area per plant and yield attributes; and chlorophyll (Chl) content, Chl_a/chlorophyllide_a (Chlid_a), and Chl_b/Chlid_b were considerably reduced within the drought condition. On the other hand, oxidative biomarkers, as well as organic and antioxidant solutes, were increased under drought, associated with membrane dysfunction, superoxide dismutase (SOD) activation, and osmotic adjustment (OA) capacity as well as a hyperaccumulation of porphyrin intermediates. Supplementation of Bc and Si lessens the detrimental impacts of drought on several plant metabolic processes associated with increasing leaf area and yield attributes. Their application under normal or drought conditions significantly elicited the accumulation of organic and antioxidant solutes as well as the activation of antioxidant enzymes, followed by lessening the formation of free radical oxygen and mitigating oxidative injuries. Moreover, their application maintained water status and OA capacity. Si and/or Bc treatment reduced protoporphyrin, magnesium-protoporphyrin, and protochlorophyllide while increasing Chl_a and Chl_b assimilation and boosting the ratio of Chl_a/Chlid_a and Chl_b/Chlid_b, resulting in a rise in leaf area per plant and yield components following these modifications. These findings highlight the significance of Si and/or Bc as (a) stress-signaling molecule(s) in regulating defensive systems in drought-affected borage plants by boosting antioxidant aptitude, regulating water status, and accelerating chlorophyll assimilation, thus leading to increasing leaf area and productivity.

The diversity of substrates for plant respiration and how to optimize their use

Plant respiration is a foundational biological process with the potential to be optimized to improve crop yield. To understand and manipulate the outputs of respiration, the inputs of respiration-respiratory substrates-need to be probed in detail. Mitochondria house substrate catabolic pathways and respiratory machinery, so transport into and out of these organelles plays an important role in committing substrates to respiration. The large number of mitochondrial carriers and catabolic pathways that remain unidentified hinder this process and lead to confusion about the identity of direct and indirect respiratory substrates in plants. The sources and usage of respiratory substrates vary and are increasing found to be highly regulated based on cellular processes and environmental factors. This review covers the use of direct respiratory substrates following transport through mitochondrial carriers and catabolism under normal and stressed conditions. We suggest the introduction of enzymes not currently found in plant mitochondria to enable serine and acetate to be direct respiratory substrates in plants. We also compare respiratory substrates by assessing energetic yields, availability in cells, and their full or partial oxidation during cell catabolism. This information can assist in decisions to use synthetic biology approaches to alter the range of respiratory substrates in plants. As a result, respiration could be optimized by introducing, improving, or controlling specific mitochondrial transporters and mitochondrial catabolic pathways.

Over-expression of the barley Phytoglobin 1 (HvPgb1) evokes leaf-specific transcriptional responses during root waterlogging

Oxygen deprivation (hypoxia) in the root due to waterlogging causes profound metabolic changes in the aerial organs depressing growth and limiting plant productivity in barley (Hordeum vulgare L.). Genome-wide analyses in waterlogged wild type (WT) barley (cv. Golden Promise) plants and plants over-expressing the phytoglobin 1 HvPgb1 [HvPgb1(OE)] were performed to determine leaf specific transcriptional responses during waterlogging. Normoxic WT plants outperformed their HvPgb1(OE) counterparts for dry weight biomass, chlorophyll content, photosynthetic rate, stomatal conductance, and transpiration. Root waterlogging severely depressed all these parameters in WT plants but not in HvPgb1(OE) plants, which exhibited an increase in photosynthetic rate. In leaftissue, root waterlogging repressed genes encoding photosynthetic components and chlorophyll biosynthetic enzymes, while induced those of reactive oxygen species (ROS)-generating enzymes. This repression was alleviated in HvPgb1(OE) leaves which also exhibited an induction of enzymes participating in antioxidant responses. In the same leaves, the transcript levels of several genes participating in nitrogen metabolism were also higher relative to WT leaves. Ethylene levels were diminished by root waterlogging in leaves of WT plants, but not in HvPgb1(OE), which were enriched in transcripts of ethylene biosynthetic enzymes and ethylene response factors. Pharmacological treatments increasing the level or action of ethylene further suggested the requirement of ethylene in plant response to root waterlogging. In natural germplasm an elevation in foliar HvPgb1 between 16h and 24h of waterlogging occurred in tolerant genotypes but not in susceptible ones. By integrating morpho-physiological parameters with transcriptome data, this study provides a framework defining leaf responses to root waterlogging and indicates that the induction of HvPgb1 may be used as a selection tool to enhance resilience to excess moisture.

Overexpression of MsSAG113 gene promotes leaf senescence in alfalfa via participating in the hormone regulatory network

Introduction

Alfalfa (Medicago sativa) is a kind of high quality leguminous forage species, which was widely cultivated in the world. Leaf senescence is an essential process in plant development and life cycle. Here, we reported the isolation and functional analysis of an alfalfa SENESCENCE-ASSOCIATED GENE113 (MsSAG113), which belongs to the PP2C family and mainly plays a role in promoting plant senescence.

Methods

In the study, Agrobacterium-mediated, gene expression analysis, next generation sequencing, DNA pull-down, yeast single hybridization and transient expression were used to identify the function of MsSAG113 gene.

Results

The MsSAG113 gene was isolated from alfalfa, and the transgenic plants were obtained by Agrobacterium-mediated method. Compared with the wildtype, transgenic plants showed premature senescence in leaves, especially when cultivated under dark conditions. Meanwhile, application of exogenous hormones ABA, SA, MeJA, obviously acclerated leaf senescence of transgenic plants. Furthermore, the detached leaves from transgenic plants turned yellow earlier with lower chlorophyll content. Transcriptome analysis identified a total of 1,392 differentially expressed genes (DEGs), involving 13 transcription factor families. Of which, 234 genes were related to phytohormone synthesis, metabolism and transduction. Pull-down assay and yeast one-hybrid assay confirmed that alfalfa zinc finger CCCH domain-containing protein 39 (MsC3H-39) could directly bind the upstream of MsSAG113 gene. In conclusion, the MsSAG113 gene plays a crucial role in promoting leaf senescence in alfalfa via participating in the hormone regulatory network.

Discussion

This provides an essential basis for further analysis on the regulatory network involving senescence-associated genes in alfalfa.

Integrated transcriptomics and miRNAomics provide insights into the complex multi-tiered regulatory networks associated with coleoptile senescence in rice

Coleoptile is the small conical, short-lived, sheath-like organ that safeguards the first leaf and shoot apex in cereals. It is also the first leaf-like organ to senesce that provides nutrition to the developing shoot and is, therefore, believed to play a crucial role in seedling establishment in rice and other grasses. Though histochemical studies have helped in understanding the pattern of cell death in senescing rice coleoptiles, genome-wide expression changes during coleoptile senescence have not yet been explored. With an aim to investigate the gene regulation underlying the coleoptile senescence (CS), we performed a combinatorial whole genome expression analysis by sequencing transcriptome and miRNAome of senescing coleoptiles. Transcriptome analysis revealed extensive reprogramming of 3439 genes belonging to several categories, the most prominent of which encoded for transporters, transcription factors (TFs), signaling components, cell wall organization enzymes, redox homeostasis, stress response and hormone metabolism. Small RNA sequencing identified 41 known and 21 novel miRNAs that were differentially expressed during CS. Comparison of gene expression and miRNA profiles generated for CS with publicly available leaf senescence (LS) datasets revealed that the two aging programs are remarkably distinct at molecular level in rice. Integration of expression data of transcriptome and miRNAome identified high confidence 140 miRNA-mRNA pairs forming 42 modules, thereby demonstrating multi-tiered regulation of CS. The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.

Comparative transcriptome analysis revealed differential gene expression involved in wheat leaf senescence between stay-green and non-stay-green cultivars

Breeders agree that leaf senescence is a favorable process for wheat seed yield improvement due to the remobilization of leaf nutrients. However, several studies have suggested that staying green may be an important strategy for further increasing wheat yields. In this study, we performed a comparative transcriptome analysis between wheat cultivars CN17 and CN19 after heading and also measured photosynthetic parameters, chlorophyll (Chl) contents, and antioxidant enzyme activities at various time points after heading. The physiological and biochemical indexes revealed that CN17 exhibited a functionally stay-green phenotype while CN19 did not. We identified a total of 24,585 and 34,410 differential expression genes between genotypes at two time-points and between time-points in two genotypes, respectively, and we also found that 3 (37.5%) genes for leaf senescence, 46 (100%) for photosynthesis - antenna protein, 33 (70.21%) for Chl metabolism and 34 (68%) for antioxidative enzyme activity were upregulated in CN17 compared with CN19 during leaf senescence, which could be regulated by the differential expression of SAG39 (senescence-associated gene 39), while 22 (100%) genes for photosynthesis - antenna proteins, 6 (46.15%) for Chl metabolism and 12 (80%) for antioxidative enzyme activity were upregulated in CN17 compared with CN19 before the onset of leaf senescence. Here, we further clarified the expression profiles of genes associated with a functional stay-green phenotype. This information provides new insight into the mechanism underlying delayed leaf senescence and a new strategy for breeders to improve wheat yields.

The apple GARP family gene MdHHO3 regulates the nitrate response and leaf senescence

The regulation of plant gene expression by nitrate is a complex regulatory process. Here, we identified 90 GARP family genes in apples by genome-wide analysis. As a member of the GARP gene family, the expression of MdHHO3 (Malus domestica HYPERSENSITIVITY TO LOW PHOSPHATE-ELICITED PRIMARY ROOT SHORTENING1 HOMOLOG 3) is upregulated under N (nitrogen) supply. The results of DNA-binding site analysis and electrophoretic mobility shift assays (EMSA) showed that MdHHO3 binds to the motif-containing GAATC. Furthermore, MdHHO3 binds to its promoter sequence and inhibits its activity. In addition, the overexpression of MdHHO3 in apple calli resulted in less accumulation of nitrate in 35S:MdHHO3-GFP calli and downregulated the expression of the nitrate transport-related genes but upregulated the expression of the nitrate assimilation-related genes. Similarly, the expression of the nitrate transport-related genes was downregulated and the expression of the nitrate assimilation-related genes was upregulated in MdHHO3 overexpression Arabidopsis and tobacco plants. Interaction experiments showed that MdHHO3 could bind to the promoter MdNRT2.1 (NITRATE TRANSPORTER 2.1) and negatively regulate its expression. Moreover, the exposure of MdHHO3-overexpressing Arabidopsis and tobacco to nitrate deficiency resulted in an early senescence phenotype as compared to the WT plants. These results show that MdHHO3 can not only negatively regulate nitrate accumulation in response to nitrate but also promote early leaf senescence under nitrate deficiency. This information may be useful to further reveal the mechanism of the nitrate response and demonstrates that nitrate deficiency induces leaf senescence in apples.

Side-chain modifications of phyllobilins may not be essential for chlorophyll degradation in Arabidopsis

Disposing efficiently and safely chlorophyll derivatives during senescence requires a coordinated pathway that is well conserved throughout green plants. The PAO/phyllobilin pathway catalyzes the degradation of the chlorophyll during senescence and allows detoxification of the pigment and its subsequent export from the chloroplast. Although most of the chloroplastic reactions involved in chlorophyll degradation are well understood, the diversity of enzymes responsible for downstream modifications of non-phototoxic phyllobilins remains to be explored. More than 40 phyllobilins have been described to date, but only three enzymes catalyzing side-chain reactions have been identified in Arabidopsis thaliana, namely, TIC55, CYP89A9, and MES16. Here, by generating a triple mutant, we evaluate the extent to which these enzymes are influencing the rate and amplitude of chlorophyll degradation at the metabolite as well as its regulation at the transcriptome level. Our data show that major side-chain modifications of phyllobilins do not influence significantly chlorophyll degradation or leaf senescence, letting the physiological relevance of their striking diversity an open question.

Know when and how to die: gaining insights into the molecular regulation of leaf senescence

Senescence is the ultimate phase in the life cycle of leaves which is crucial for recycling of nutrients to maintain plant fitness and reproductive success. The earliest visible manifestation of leaf senescence is their yellowing, which usually commences with the breakdown of chlorophyll. The degradation process involves a gradual and highly coordinated disassembly of macromolecules resulting in the accumulation of nutrients, which are subsequently mobilized from the senescing leaves to the developing organs. Leaf senescence progresses under overly tight genetic and molecular control involving a well-orchestrated and intricate network of regulators that coordinate spatio-temporally with the influence of both internal and external cues. Owing to the advancements in omics technologies, the availability of mutant resources, scalability of molecular analyses methodologies and the advanced capacity to integrate multidimensional data, our understanding of the genetic and molecular basis of leaf ageing has greatly expanded. The review provides a compilation of the multitier regulation of senescence process and the interrelation between the environment and the terminal phase of leaf development. The knowledge gained would benefit in devising the strategies for manipulation of leaf senescence process to improve crop quality and productivity.

Short daily ultraviolet exposure enhances intrinsic water-use efficiency and delays senescence in Micro-Tom tomato plants

Ultraviolet (UV) radiation, unless present at high doses, is recognised as a regulator of plant growth and some specific processes. The present study investigated the influence of short daily UV irradiation (15min/day, 11days) on leaf gas exchange and some biochemical and molecular markers of leaf senescence (such as stomata movements, chlorophyll breakdown, anthocyanin production, senescence-associated genes) in Micro-Tom tomato plants. The UV-induced reduction of g s (stomatal conductance) during the treatment was associated with the modified expression of some genes involved in the control of stomatal movements. We hypothesise a two-step regulation of stomatal closure involving salicylic and abscisic acid hormones. The temporal changes of g s and A net (net photosynthetic CO2 assimilation rate) along with the pigment behaviour, suggest a possible delay of leaf senescence in treated plants, confirmed by the expression levels of genes related to senescence such as SAG113 and DFR . The UV potential to induce a persistent partial inhibition of g s without severely affecting A net led to an increased iWUE (intrinsic water-use efficiency) during the 11-day treatment, suggesting a priming effect of short daily UV radiation towards drought conditions potentially useful in reducing the excess water use in agriculture.

Induction and Characterization of Tetraploid Through Zygotic Chromosome Doubling in Eucalyptus urophylla

Improvements in plant growth can bring great benefits to the forest industry. Eucalyptus urophylla is an important plantation species worldwide, and given that ploidy increases are often associated with plant phenotype changes, it was reasoned that its polyploidization may have good prospects and great significance toward its cultivation. In this study, the zygotic development period of E. urophylla was observed through paraffin sections, and a correlation between the development time of flower buds after pollination and the zygotic development period was established. On this basis, it was determined that the 25th day after pollination was the appropriate time for a high temperature to induce zygotic chromosome doubling. Then tetraploid E. urophylla was successfully obtained for the first time through zygotic chromosome doubling induced by high temperature, and the appropriate conditions were treating flower branches at 44°C for 6 h. The characterization of tetraploid E. urophylla was performed. Chromosome duplication brought about slower growing trees with thicker leaves, larger cells, higher net photosynthetic rates, and a higher content of certain secondary metabolites. Additionally, the molecular mechanisms for the variation in the tetraploid's characteristics were studied. The qRT-PCR results showed that genes mediating the tetraploid characteristics showed the same change trend as those of the characteristics, which verified that tetraploid trait variation was mainly caused by gene expression changes. Furthermore, although the tetraploid had no growth advantage compared with the diploid, it can provide important germplasm resources for future breeding, especially for the creation of triploids.

Phytochrome B Conveys Low Ambient Temperature Cues to the Ethylene-Mediated Leaf Senescence in Arabidopsis

Leaf senescence is an active developmental process that is tightly regulated through extensive transcriptional and metabolic reprogramming events, which underlie controlled degradation and relocation of nutrients from aged or metabolically inactive leaves to young organs. The onset of leaf senescence is coordinately modulated by intrinsic aging programs and environmental conditions, such as prolonged darkness and temperature extremes. Seedlings growing under light deprivation, as often experienced in severe shading or night darkening, exhibit an accelerated senescing process, which is mediated by a complex signaling network that includes sugar starvation responses and light signaling events via the phytochrome B (phyB)-PHYTOCHROME-INTERACTING FACTOR (PIF) signaling routes. Notably, recent studies indicate that nonstressful ambient temperatures profoundly influence the onset and progression of leaf senescence in darkness, presumably mediated by the phyB-PIF4 signaling pathways. However, it is not fully understood how temperature signals regulate leaf senescence at the molecular level. Here, we demonstrated that low ambient temperatures repress the nuclear export of phyB and the nuclear phyB suppresses the transcriptional activation activity of ethylene signaling mediator ETHYLENE INSENSITIVE3 (EIN3), thus delaying leaf senescence. Accordingly, leaf senescence was insensitive to low ambient temperatures in transgenic plants overexpressing a constitutively nuclear phyB form, as observed in ein3 eil1 mutants. In contrast, leaf senescence was significantly promoted in phyB-deficient mutants under identical temperature conditions. Our data indicate that phyB coordinately integrates light and temperature cues into the EIN3-mediated ethylene signaling pathway that regulates leaf senescence under light deprivation, which would enhance plant fitness under fluctuating natural environments.

2-Hydroxy-phytanoyl-CoA lyase (AtHPCL) is involved in phytol metabolism in Arabidopsis

During chlorophyll degradation, large amounts of the isoprenoid alcohol phytol are released. The pathway of phytol catabolism has been studied in humans, because chlorophyll is part of the human diet, but little is known for plants. In humans, phytanoyl-CoA derived from phytol is degraded via α-oxidation by phytanoyl-CoA hydroxylase (PAHX) and 2-hydroxy-phytanoyl-CoA lyase (HPCL). Arabidopsis contains two sequences homologous to the human proteins AtPAHX and AtHPCL. Insertional mutants of Arabidopsis (pahx, hpcl) were grown under N deprivation to stimulate chlorophyll breakdown or supplemented with phytol to increase the endogenous amount of phytol. During N deprivation, chlorophyll, phytol, phytenal, upstream metabolites of phytol breakdown, and tocopherol and fatty acid phytyl esters, alternative phytol-derived lipids, accumulated in pahx and hpcl mutants, in line with the scenario that the mutations interfere with phytol degradation. AtHPCL was localized to the peroxisomes. Expression analysis of the AtHPCL sequence in the yeast Δpxp1 or Δmpo1 mutants followed by supplementation with 2-hydroxy-palmitic acid and enzyme assays of peroxisomal proteins from Col-0 and hpcl plants with 2-hydroxy-stearoyl-CoA revealed that AtHPCL harbors 2-hydroxy-acyl-CoA lyase activity. The α-dioxygenases αDOX1 and αDOX2 are involved in α-oxidation of fatty acids and could be involved in an alternative pathway of phytol degradation. However, phytol-related lipids in the αdox1, αdox2, or αdox1 αdox2 mutants were not altered compared with Col-0, indicating that αDOX1 and αDOX2 are not involved in phytol degradation. These results demonstrate that phytol degradation in Arabidopsis involves α-oxidation by AtPAHX and AtHPCL, but that it is independent of αDOX1/αDOX2.

Evolution of chlorophyll degradation is associated with plant transition to land

Chlorophyll, the central pigment of photosynthesis, is highly photo‐active and degraded enzymatically during leaf senescence. Merging comparative genomics and metabolomics, we evaluate the extent to which the chlorophyll detoxification pathway has evolved in Viridiplantae. We argue that cytosolic detoxification of phyllobilins in particular was a critical process to the green lineage’s transition to land.

Core Components of Abscisic Acid Signaling and Their Post-translational Modification

Abscisic acid (ABA) is a major phytohormone that regulates plant growth, development, and abiotic/biotic stress responses. Under stress, ABA is synthesized in various plant organs, and it plays roles in diverse adaptive processes, including seed dormancy, growth inhibition, and leaf senescence, by modulating stomatal closure and gene expression. ABA receptor, clade A protein phosphatase 2C (PP2C), and SNF1-related protein kinase 2 (SnRK2) proteins have been identified as core components of ABA signaling, which is initiated via perception of ABA with receptor and subsequent activation or inactivation by phosphorylation/dephosphorylation. The findings of several recent studies have established that the post-translational modification of these components, including phosphorylation and ubiquitination/deubiquitination, play important roles in regulating their activity and stability. In this review, we discuss the functions of the core components of ABA signaling and the regulation of their activities via post-translational modification under normal and stress conditions.

The miR528-AO Module Confers Enhanced Salt Tolerance in Rice by Modulating the Ascorbic Acid and Abscisic Acid Metabolism and ROS Scavenging

The monocot lineage-specific miR528 was previously established as a multistress regulator. However, it remains largely unclear how miR528 participates in response to salinity stress in rice. Here, we show that miR528 positively regulates rice salt tolerance by down-regulating a gene encoding l-ascorbate oxidase (AO), thereby bolstering up the AO-mediated abscisic acid (ABA) synthesis and ROS scavenging. Overexpression of miR528 caused a substantial increase in ascorbic acid (AsA) and ABA contents but a significant reduction in ROS accumulation, resulting in the enhanced salt tolerance of rice plants. Conversely, knockdown of miR528 or overexpression of AO stimulated the expression of the AO gene, hence lowering the level of AsA, a critical antioxidant that promotes the ABA content but reduces the ROS level, and then compromising rice tolerance to salinity. Together, the findings reveal a novel mechanism of the miR528-AO module-mediated salt tolerance by modulating the processes of AsA and ABA metabolism as well as ROS detoxification, which adds a new regulatory role to the miR528-AO stress defense pathway in rice.

The apple C2H2-type zinc finger transcription factor MdZAT10 positively regulates JA-induced leaf senescence by interacting with MdBT2

Jasmonic acid (JA) plays an important role in regulating leaf senescence. However, the molecular mechanisms of leaf senescence in apple (Malus domestica) remain elusive. In this study, we found that MdZAT10, a C2H2-type zinc finger transcription factor (TF) in apple, markedly accelerates leaf senescence and increases the expression of senescence-related genes. To explore how MdZAT10 promotes leaf senescence, we carried out liquid chromatography/mass spectrometry screening. We found that MdABI5 physically interacts with MdZAT10. MdABI5, an important positive regulator of leaf senescence, significantly accelerated leaf senescence in apple. MdZAT10 was found to enhance the transcriptional activity of MdABI5 for MdNYC1 and MdNYE1, thus accelerating leaf senescence. In addition, we found that MdZAT10 expression was induced by methyl jasmonate (MeJA), which accelerated JA-induced leaf senescence. We also found that the JA-responsive protein MdBT2 directly interacts with MdZAT10 and reduces its protein stability through ubiquitination and degradation, thereby delaying MdZAT10-mediated leaf senescence. Taken together, our results provide new insight into the mechanisms by which MdZAT10 positively regulates JA-induced leaf senescence in apple.

An evergreen mind and a heart for the colors of fall

With the finest biochemical and molecular approaches, convincing explorative strategies, and long-term vision, Stefan Hörtensteiner succeeded in elucidating the biochemical pathway responsible for chlorophyll degradation. After having contributed to the identification of key chlorophyll degradation products in the course of the past 25 years, he gradually identified and characterized most of the crucial players in the PAO/phyllobilin degradation pathway of chlorophyll. He was one of the brightest plant biochemists of his generation, and his work opened doors to a better understanding of plant senescence, tetrapyrrole homeostasis, and their complex regulation. He sadly passed away on 5 December 2020, aged 57.

Phyllobilins as a challenging diverse natural product class: Exploration of pharmacological activities

Phyllobilins are a group of chlorophyll-derived bilin-type linear tetrapyrroles, generated in the process of chlorophyll breakdown. Since the first phyllobilin was isolated and characterized in 1991, more and more structures of these chlorophyll catabolites were identified alongside the biochemical players involved in chlorophyll breakdown. In the meantime, phyllobilins are known to occur in a large natural structural variety, and new modifications are still being discovered. Phyllobilins have been regarded as products of chlorophyll detoxification for a very long time, hence they have been completely overlooked as a natural product class in terms of their biological role or pharmacological activity. A change of this paradigm, however, is long overdue. Here, we review the current knowledge of the pharmacological activities of phyllobilins and give an overview of the diverse structural modifications, laying the groundwork for analyzing their role(s) as active components in medicinal plants.

Leaf senescence: progression, regulation, and application

Leaf senescence, the last stage of leaf development, is a type of postmitotic senescence and is characterized by the functional transition from nutrient assimilation to nutrient remobilization which is essential for plants' fitness. The initiation and progression of leaf senescence are regulated by a variety of internal and external factors such as age, phytohormones, and environmental stresses. Significant breakthroughs in dissecting the molecular mechanisms underpinning leaf senescence have benefited from the identification of senescence-altered mutants through forward genetic screening and functional assessment of hundreds of senescence-associated genes (SAGs) via reverse genetic research in model plant Arabidopsis thaliana as well as in crop plants. Leaf senescence involves highly complex genetic programs that are tightly tuned by multiple layers of regulation, including chromatin and transcription regulation, post-transcriptional, translational and post-translational regulation. Due to the significant impact of leaf senescence on photosynthesis, nutrient remobilization, stress responses, and productivity, much effort has been made in devising strategies based on known senescence regulatory mechanisms to manipulate the initiation and progression of leaf senescence, aiming for higher yield, better quality, or improved horticultural performance in crop plants. This review aims to provide an overview of leaf senescence and discuss recent advances in multi-dimensional regulation of leaf senescence from genetic and molecular network perspectives. We also put forward the key issues that need to be addressed, including the nature of leaf age, functional stay-green trait, coordination between different regulatory pathways, source-sink relationship and nutrient remobilization, as well as translational researches on leaf senescence.

Comparative Transcriptome-Based Mining of Senescence-Related MADS, NAC, and WRKY Transcription Factors in the Rapid-Senescence Line DLS-91 of Brassica rapa

Leaf senescence is a developmental process induced by various molecular and environmental stimuli that may affect crop yield. The dark-induced leaf senescence-91 (DLS-91) plants displayed rapid leaf senescence, dramatically decreased chlorophyll contents, low photochemical efficiencies, and upregulation of the senescence-associated marker gene BrSAG12-1. To understand DLS molecular mechanism, we examined transcriptomic changes in DLS-91 and control line DLS-42 following 0, 1, and 4 days of dark treatment (DDT) stages. We identified 501, 446, and 456 DEGs, of which 16.7%, 17.2%, and 14.4% encoded TFs, in samples from the three stages. qRT-PCR validation of 16 genes, namely, 7 MADS, 6 NAC, and 3 WRKY, suggested that BrAGL8-1, BrAGL15-1, and BrWRKY70-1 contribute to the rapid leaf senescence of DLS-91 before (0 DDT) and after (1 and 4 DDT) dark treatment, whereas BrNAC046-2, BrNAC029-2/BrNAP, and BrNAC092-1/ORE1 TFs may regulate this process at a later stage (4 DDT). In-silico analysis of cis-acting regulatory elements of BrAGL8-1, BrAGL42-1, BrNAC029-2, BrNAC092-1, and BrWRKY70-3 of B. rapa provides insight into the regulation of these genes. Our study has uncovered several AGL-MADS, WRKY, and NAC TFs potentially worthy of further study to understand the underlying mechanism of rapid DLS in DLS-91.

Arabidopsis FAR-RED ELONGATED HYPOCOTYL3 negatively regulates carbon starvation responses

Light is one of the most important environmental factors that affects various cellular processes in plant growth and development; it is also crucial for the metabolism of carbohydrates as it provides the energy source for photosynthesis. Under extended darkness conditions, carbon starvation responses are triggered by depletion of stored energy. Although light rapidly inhibits starvation responses, the molecular mechanisms by which light signalling affects this process remain largely unknown. In this study, we showed that the Arabidopsis thaliana light signalling protein FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1) are essential for plant survival after extended darkness treatment at both seedling and adult stages. Transmission electron microscopy analyses revealed that disruption of both FHY3 and FAR1 resulted in destruction of chloroplast envelopes and thylakoid membranes under extended darkness conditions. Furthermore, treatment with sucrose, but not glucose, completely rescued carbon starvation-induced cell death in the rosette leaves and arrested early seedling establishment in the fhy3 far1 plants. We thus concluded that the light signalling proteins FHY3 and FAR1 negatively regulate carbon starvation responses in Arabidopsis.

Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage (Brassica rapa L.) during vernalization

BACKGROUND

Vernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Although rapid bolting and flowering promote the reproduction of Chinese cabbages (Brassica rapa L. ssp. pekinensis), this process causes their commercial value to decline. Clarifying the mechanisms of vernalization is essential for its further application. We performed RNA sequencing of gradient-vernalization in order to explore the reasons for the different bolting process of two Chinese cabbage accessions during vernalization.

RESULTS

There was considerable variation in gene expression between different-bolting Chinese cabbage accessions during vernalization. Comparative transcriptome analysis and weighted gene co-expression network analysis (WGCNA) were performed for different-bolting Chinese cabbage during different vernalization periods. The biological function analysis and hub gene annotation of highly relevant modules revealed that shoot system morphogenesis and polysaccharide and sugar metabolism caused early-bolting 'XBJ' to bolt and flower faster; chitin, ABA and ethylene-activated signaling pathways were enriched in late-bolting 'JWW'; and leaf senescence and carbohydrate metabolism enrichment were found in the two Chinese cabbage-related modules, indicating that these pathways may be related to bolting and flowering. The high connectivity of hub genes regulated vernalization, including MTHFR2, CPRD49, AAP8, endoglucanase 10, BXLs, GATLs, and WRKYs. Additionally, five genes related to flower development, BBX32 (binds to the FT promoter), SUS1 (increases FT expression), TSF (the closest homologue of FT), PAO and NAC029 (plays a role in leaf senescence), were expressed in the two Chinese cabbage accessions.

CONCLUSION

The present work provides a comprehensive overview of vernalization-related gene networks in two different-bolting Chinese cabbages during vernalization. In addition, the candidate pathways and hub genes related to vernalization identified here will serve as a reference for breeders in the regulation of Chinese cabbage production.

Phytol derived from chlorophyll hydrolysis in plants is metabolized via phytenal

Phytol is the isoprenoid alcohol bound in ester linkage to chlorophyll, the most abundant photosynthetic pigment in plants. During leaf senescence, large amounts of phytol are released by chlorophyll degradation. However, the pathway of phytol catabolism in plants is unknown. We hypothesized that phytol degradation in plants might involve its oxidation into the long-chain aldehyde phytenal. Using GC-MS for aldehyde quantification after derivatization with methylhydroxylamine, phytenal was identified in leaves, whereas other long-chain aldehydes (phytanal and pristanal) were barely detectable. We found that phytenal accumulates during chlorotic stresses, for example, salt stress, dark-induced senescence, and nitrogen deprivation. The increase in the phytenal content is mediated at least in part independently of enzyme activities, and it is independent of light. Characterization of phytenal accumulation in the pao1 mutant affected in chlorophyll degradation revealed that phytenal is an authentic phytol metabolite derived from chlorophyll breakdown. The increase in phytenal was even stronger in mutants affected in the production of other phytol metabolites including vte5-2 (tocopherol deficient) and pes1 pes2 (fatty acid phytyl ester deficient). Therefore, phytenal accumulation is controlled by competing, alternative pathways of phosphorylation (leading to tocopherol production) or esterification (fatty acid phytyl ester production). As a consequence, the content of phytenal is maintained at low levels, presumably to minimize its toxic effects caused by its highly reactive aldehyde group that can form covalent bonds with and inactivate the amino groups of proteins.

When a knockout is an Achilles' heel: Resistance to one potyvirus species triggers hypersusceptibility to another one in Arabidopsis thaliana

The translation initiation factors 4E are a small family of major susceptibility factors to potyviruses. It has been suggested that knocking out these genes could provide genetic resistance in crops when natural resistance alleles, which encode functional eIF4E proteins, are not available. Here, using the well-characterized Arabidopsis thaliana-potyvirus pathosystem, we evaluate the resistance spectrum of plants knocked out for eIF4E1, the susceptibility factor to clover yellow vein virus (ClYVV). We show that besides resistance to ClYVV, the eIF4E1 loss of function is associated with hypersusceptibility to turnip mosaic virus (TuMV), a potyvirus known to rely on the paralog host factor eIFiso4E. On TuMV infection, plants knocked out for eIF4E1 display striking developmental defects such as early senescence and primordia development stoppage. This phenotype is coupled with a strong TuMV overaccumulation throughout the plant, while remarkably the levels of the viral target eIFiso4E remain uninfluenced. Our data suggest that this hypersusceptibility cannot be explained by virus evolution leading to a gain of TuMV aggressiveness. Furthermore, we report that a functional eIF4E1 resistance allele engineered by CRISPR/Cas9 base-editing technology successfully circumvents the increase of TuMV susceptibility conditioned by eIF4E1 disruption. These findings in Arabidopsis add to several previous findings in crops suggesting that resistance based on knocking out eIF4E factors should be avoided in plant breeding, as it could also expose the plant to the severe threat of potyviruses able to recruit alternative eIF4E copies. At the same time, it provides a simple model that can help understanding of the homeostasis among eIF4E proteins in the plant cell and what makes them available to potyviruses.

Arabidopsis Phototropins Participate in the Regulation of Dark-Induced Leaf Senescence

Senescence is the final stage of plant development, affecting individual organs or the whole organism, and it can be induced by several environmental factors, including shading or darkness. Although inevitable, senescence is a complex and tightly regulated process, ensuring optimal remobilization of nutrients and cellular components from senescing organs. Photoreceptors such as phytochromes and cryptochromes are known to participate in the process of senescence, but the involvement of phototropins has not been studied to date. We investigated the role of these blue light photoreceptors in the senescence of individually darkened Arabidopsis thaliana leaves. We compared several physiological and molecular senescence markers in darkened leaves of wild-type plants and phototropin mutants (phot1, phot2, and phot1phot2). In general, all the symptoms of senescence (lower photochemical activity of photosystem II, photosynthetic pigment degradation, down-regulation of photosynthetic genes, and up-regulation of senescence-associated genes) were less pronounced in phot1phot2, as compared to the wild type, and some also in one of the single mutants, indicating delayed senescence. This points to different mechanisms of phototropin operation in the regulation of senescence-associated processes, either with both photoreceptors acting redundantly, or only one of them, phot1, playing a dominant role.

Genetic regulation of the traits contributing to wheat nitrogen use efficiency

High nitrogen application aimed at increasing crop yield is offset by higher production costs and negative environmental consequences. For wheat, only one third of the applied nitrogen is utilized, which indicates there is scope for increasing Nitrogen Use Efficiency (NUE). However, achieving greater NUE is challenged by the complexity of the trait, which comprises processes associated with nitrogen uptake, transport, reduction, assimilation, translocation and remobilization. Thus, knowledge of the genetic regulation of these processes is critical in increasing NUE. Although primary nitrogen uptake and metabolism-related genes have been well studied, the relative influence of each towards NUE is not fully understood. Recent attention has focused on engineering transcription factors and identification of miRNAs acting on expression of specific genes related to NUE. Knowledge obtained from model species needs to be translated into wheat using recently-released whole genome sequences, and by exploring genetic variations of NUE-related traits in wild relatives and ancient germplasm. Recent findings indicate the genetic basis of NUE is complex. Pyramiding various genes will be the most effective approach to achieve a satisfactory level of NUE in the field.

The fate of chlorophyll in phytophagous insects goes beyond nutrition

Chlorophyll (Chl) is a natural compound that is found in all autotrophic plants. Since phytophagous insects ingest the photosynthetically active material with the plant leaves, the question arises if and how herbivores deal with Chl and its degradation products. Here we review findings on Chl degradation in phytophagous insects and highlight the role of these ubiquitous plant metabolites for plant-feeding insects. Due to the anaerobic gut of many insects, the degradation is limited to the removal of the peripheral substituents, while the tetrapyrrole core remains intact. Proteins, such as red fluorescent protein, P252 (a novel 252-kDa protein), and chlorophyllide binding protein have been reported to occur in the insect gut and might be indirectly connected to Chl degradation. Besides of an nutritional value, e.g., by taking up Mg²⁺ ions or by sequestration of carbon from the phytol side chain, the Chl degradation products may serve the insect, after binding to certain proteins, as antimicrobial, antifungal, and antiviral factors. The protein complexes may also confer protection against reactive oxygen species. The antibiotic potential of proteins and degradation products does not only benefit phytophagous insects but also human being in medical application of cancer treatment for instance. This review highlights these aspects from a molecular, biochemical, and ecological point of view.

Chlorophyll dephytylation in chlorophyll metabolism: a simple reaction catalyzed by various enzymes

Chlorophyll (Chl) is composed of a tetrapyrrole ring and a phytol tail, which facilitate light energy absorbance and assembly with photosynthetic protein complexes, respectively. Chl dephytylation, the hydrolytic removal of the phytol tail, is considered a pivotal step in diverse physiological processes, such as Chl salvage during repair of the photosystem, the Chl cycle in the adjustment of antenna size, and Chl breakdown in leaf senescence and fruit maturation. Moreover, phytol is a component of the tocopherols, a major form of vitamin E that is essential in the human diet. This phytol mostly comes from Chl hydrolysis. However, the authentic enzyme responsible for Chl dephytylation has proved elusive. CHLOROPHYLLASE (CLH) which was discovered over a century ago, was the first enzyme found to have dephytylation activity in vitro, but its role in Chl metabolism has been questioned and remains under debate. Recently, novel dephytylases, i.e., PHEOPHYTINASE (PPH) and CHLOROPHYLL DEPHYTYLASE1 (CLD1) have emerged from genetic studies, indicating that dephytylation in Chl catabolism involves different players and is more complicated than previously thought. Based on sequence homology, substrate specificity, and subcellular localization, CLH, PPH, and CLD1 belong to different types of dephytylase, which prompted us to re-examine the dilemmas and missing links that still exist in Chl metabolism. This review thus focuses on the hitherto unanswered questions involving the Chl dephytylation reaction by highlighting relevant literature, updating recent progress, and synthesizing ideas.

A mitochondrial prolyl aminopeptidase PAP2 releases N-terminal proline and regulates proline homeostasis during stress response

Most mitochondrial proteins are synthesised in the cytosol and targeted into the organelle via N-terminal targeting peptides that are cleaved upon import. The free targeting peptide is subsequently processed in a stepwise manner, with single amino acids released as final products. Here, we have characterised a proline-cleaving aminopeptidase in Arabidopsis thaliana, prolyl aminopeptidase-2 (PAP2, At3g61540). Activity assays show that PAP2 has a preferred activity to hydrolyse N-terminal proline. Protein localisation studies revealed that PAP2 is exclusively targeted to mitochondria. Characterisation of pap2 mutants show defective pollen, enhanced dark-induced senescence and increased susceptibility to abiotic stresses, which are likely attributed to a reduced level of accumulated free proline. Taken together, these results demonstrate the role of PAP2 in proline cleavage from mitochondrial peptides and proline homeostasis, which is required for the development of male gametophyte, tolerance to abiotic stresses, and leaf senescence.

RdDM pathway components differentially modulate Tobamovirus symptom development

The crop yield losses induced by phytoviruses are mainly associated with the symptoms of the disease. DNA modifications as methylation can modulate the information coded by the sequence, process named epigenetics. Viral infection can change the expression patterns of different genes linked to defenses and symptoms. This work represents the initial step to expose the role of epigenetic process, in the production of symptoms associated with plants-virus interactions. Small RNAs (sRNAs) are important molecules for gene regulation in plants and play an essential role in plant-pathogen interactions. Researchers have evaluated the relationship between viral infections as well as the endogenous accumulation of sRNAs and the transcriptional changes associated with the production of symptoms, but little is known about a possible direct role of epigenetics, mediated by 24-nt sRNAs, in the induction of these symptoms. Using different RNA directed DNA methylation (RdDM) pathway mutants and a triple demethylase mutant; here we demonstrate that the disruption of RdDM pathway during viral infection produce alterations in the plant transcriptome and in consequence changes in plant symptoms. This study represents the initial step in exposing that DNA methylation directed by endogenous sRNAs has an important role, uncoupled to defense, in the production of symptoms associated with plant-virus interactions.

Seedling Chloroplast Responses Induced by N-Linolenoylethanolamine Require Intact G-Protein Complexes

In animals, several long-chain N-acylethanolamines (NAEs) have been identified as endocannabinoids and are autocrine signals that operate through cell surface G-protein-coupled cannabinoid receptors. Despite the occurrence of NAEs in land plants, including nonvascular plants, their precise signaling properties and molecular targets are not well defined. Here we show that the activity of N-linolenoylethanolamine (NAE 18:3) requires an intact G-protein complex. Specifically, genetic ablation of the Gβγ dimer or loss of the full set of atypical Gα subunits strongly attenuates an NAE-18:3-induced degreening of cotyledons in Arabidopsis (Arabidopsis thaliana) seedlings. This effect involves, at least in part, transcriptional regulation of chlorophyll biosynthesis and catabolism genes. In addition, there is feedforward transcriptional control of G-protein signaling components and G-protein interactors. These results are consistent with NAE 18:3 being a lipid signaling molecule in plants with a requirement for G-proteins to mediate signal transduction, a situation similar, but not identical, to the action of NAE endocannabinoids in animal systems.

SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue

BACKGROUND

As a cool-season grass species, tall fescue (Festuca arundinacea) is challenged by increasing temperatures. Heat acclimation or activation of leaf senescence, are two main strategies when tall fescue is exposed to heat stress (HS). However, lacking a genome sequence, the complexity of hexaploidy nature, and the short read of second-generation sequencing hinder a comprehensive understanding of the mechanism. This study aims to characterize the molecular mechanism of heat adaptation and heat-induced senescence at transcriptional and post-transcriptional levels.

RESULTS

Transcriptome of heat-treated (1 h and 72 h) and senescent leaves of tall fescue were generated by combining single-molecular real-time and Illumina sequencing. In total, 4076; 6917, and 11,918 differentially expressed genes (DEGs) were induced by short- and long-term heat stress (HS), and senescence, respectively. Venn and bioinformatics analyses of DEGs showed that short-term HS strongly activated heat shock proteins (Hsps) and heat shock factors (Hsfs), as well as specifically activated FK506-binding proteins (FKBPs), calcium signaling genes, glutathione S-transferase genes, photosynthesis-related genes, and phytohormone signaling genes. By contrast, long-term HS shared most of DEGs with senescence, including the up-regulated chlorophyll catabolic genes, phytohormone synthesis/degradation genes, stress-related genes, and NACs, and the down-regulated photosynthesis-related genes, FKBPs, and catalases. Subsequently, transient overexpression in tobacco showed that FaHsfA2a (up-regulated specifically by short-term HS) reduced cell membrane damages caused by HS, but FaNAC029 and FaNAM-B1 (up-regulated by long-term HS and senescence) increased the damages. Besides, alternative splicing was widely observed in HS and senescence responsive genes, including Hsps, Hsfs, and phytohormone signaling/synthesis genes.

CONCLUSIONS

The short-term HS can stimulate gene responses and improve thermotolerance, but long-term HS is a damage and may accelerate leaf senescence. These results contribute to our understanding of the molecular mechanism underlying heat adaptation and heat-induced senescence.

Involvement of CsERF2 in leaf variegation of Cymbidium sinense 'Dharma'

MAIN CONCLUSION

CsERF2, an ethylene response factor, plays a role in leaf variegation. Leaf variegation is a main ornamental characteristic in Cymbidium sinense (C. sinense). However, the mechanisms of leaf color variegation remain largely unclear. In the present study, we analyzed the cytological and physiological features, as well as molecular analyses of leaves from wild-type (WT) and leaf variegation mutants of Cymbidium sinense 'Dharma'. Chloroplasts with typical and functional structures were discovered in WT and green sectors of the mutants leaves (MG), but not in yellow sectors of the mutant leaves (MY). The activities of key enzymes involved in chlorophyll (Chl) degradation and their substrate contents were significantly increased in MY. Genes related to Chl degradation also showed a significant up-regulation in MY. Transcriptomic analysis showed that the expression of all identified ethylene response factors (ERFs) was significantly up-regulated, and the 1-aminocyclopropane-1-carboxylic acid (ACC) content in MY was significantly higher compared with MG. QRT-PCR analysis validated that the expression levels of genes related to Chl degradation could be positively affected by ethylene (ETH) treatment. Stable overexpression of CsERF2 in Nicotiana tabacum (N. tabacum) led to a decrease in Chl content and abnormal chloroplast. Transcriptomic analysis and qRT-PCR results showed that the KEGG pathway related to chloroplast development and function showed significant change in transgenic N. tabacum. Therefore, the leaf color formation of C. sinense was greatly affected by chloroplast development and Chl metabolism. CsERF2 played an important role in leaf variegation of C. sinense.

Foliar application of melatonin delay leaf senescence in maize by improving the antioxidant defense system and enhancing photosynthetic capacity under semi-arid regions

Melatonin is an important plant growth regulator which plays a key role in plant growth and development. The objective of the current research was to evaluate the effect of foliar application of melatonin (MF) on photosynthetic efficiency, antioxidant defense mechanism, and its relation with leaf senescence in maize crop grown in a semi-arid region. A field experiment was conducted during 2017 and 2018 growth season, where melatonin was applied to the foliage at concentrations of 0 (MF₀), 25 (MF₁), 50 (MF₂), and 75 (MF₃) μM at the ninth leaf stage. Foliar application of melatonin significantly improved chlorophyll content, net photosynthetic rate, soluble sugar content, and soluble protein content during the process of leaf senescence. The application of melatonin also enhanced antioxidant enzyme activities including superoxide dismutase, catalase, and peroxidase, while reduced malondialdehyde and reactive oxygen species accumulation. Melatonin foliar application also increased total leaf area per plant, grains per ear, thousand grain weight and grain yield of maize crop in a semi-arid region. The application of melatonin significantly improved photosynthetic activity, antioxidant defense mechanism, and yield of maize crop in a semi-arid region, where the most effective treatment was MF2.

Biochemical and Comparative Transcriptome Analyses Reveal Key Genes Involved in Major Metabolic Regulation Related to Colored Leaf Formation in Osmanthus fragrans 'Yinbi Shuanghui' during Development

Osmanthus fragrans 'Yinbi Shuanghui' not only has a beautiful shape and fresh floral fragrance, but also rich leaf colors that change, making the tree useful for landscaping. In order to study the mechanisms of color formation in O. fragrans 'Yinbi Shuanghui' leaves, we analyzed the colored and green leaves at different developmental stages in terms of leaf pigment content, cell structure, and transcriptome data. We found that the chlorophyll content in the colored leaves was lower than that of green leaves throughout development. By analyzing the structure of chloroplasts, the colored leaves demonstrated more stromal lamellae and low numbers of granum thylakoid. However, there was a large number of plastoglobuli. Using transcriptome sequencing, we demonstrated that the expression of differentially expressed genes (DEGs) involved in chlorophyll degradation was upregulated, i.e., heme oxygennase-1 (HO1), pheophorbide a oxidase (PAO), and chlorophyllase-2 (CLH2), affecting the synthesis of chlorophyll in colored leaves. The stay-green gene (SGR) was upregulated in colored leaves. Genes involved in carotenoid synthesis, i.e., phytoene synthase 1 (PSY1) and 1-Deoxyxylulose-5-phosphate synthase (DXS), were downregulated in colored leaves, impeding the synthesis of carotenoids. In the later stage of leaf development, the downregulated expression of Golden2-Like (GLK) inhibited chloroplast development in colored leaves. Using weighted gene co-expression network analysis (WGCNA) to investigate the correlation between physiological indicators and DEGs, we chose the modules with the highest degree of relevance to chlorophyll degradation and carotenoid metabolism. A total of five genes (HSFA2, NFYC9, TCP20, WRKY3, and WRKY4) were identified as hub genes. These analyses provide new insights into color formation mechanisms in O. fragrans 'Yinbi Shuanghui' leaves at the transcriptional level.

Post-translational coordination of chlorophyll biosynthesis and breakdown by BCMs maintains chlorophyll homeostasis during leaf development

Chlorophyll is indispensable for life on Earth. Dynamic control of chlorophyll level, determined by the relative rates of chlorophyll anabolism and catabolism, ensures optimal photosynthesis and plant fitness. How plants post-translationally coordinate these two antagonistic pathways during their lifespan remains enigmatic. Here, we show that two Arabidopsis paralogs of BALANCE of CHLOROPHYLL METABOLISM (BCM) act as functionally conserved scaffold proteins to regulate the trade-off between chlorophyll synthesis and breakdown. During early leaf development, BCM1 interacts with GENOMES UNCOUPLED 4 to stimulate Mg-chelatase activity, thus optimizing chlorophyll synthesis. Meanwhile, BCM1’s interaction with Mg-dechelatase promotes degradation of the latter, thereby preventing chlorophyll degradation. At the onset of leaf senescence, BCM2 is up-regulated relative to BCM1, and plays a conserved role in attenuating chlorophyll degradation. These results support a model in which post-translational regulators promote chlorophyll homeostasis by adjusting the balance between chlorophyll biosynthesis and breakdown during leaf development.

Plants regulate chlorophyll levels to optimise photosynthesis. Here Wang et al. describe two paralogous thylakoid proteins, BCM1 and BCM2, which stimulate chlorophyll biosynthesis and attenuate chlorophyll degradation respectively through interaction with the Mg-chelatase-stimulating factor GUN4 and Mg-dechelatase isoform SGR1.

Toxicity of the herbicide flurochloridone to the aquatic plants Ceratophyllum demersum and Lemna minor

As a new and efficient selective pre-emergence herbicide, flurochloridone (FLC) has been widely promoted in recent years but readily results in residues in nature. As the primary producers and restorers of the water environment, aquatic plants are at risk of FLC exposure. In the present research, we studied the phytotoxicity of FLC in Lemna minor and Ceratophyllum demersum. The physiological and growth responses of these two aquatic plants exposed to different concentrations of FLC (0, 20, 100, 300, 1000, and 2000 μg/L) were measured. The results showed that FLC (≥ 20 μg/L) could cause serious photosynthesis pigment damage and bleaching in C. demersum and L. minor. Significant oxidative damage was observed in L. minor at 20 μg/L FLC, while there was no severe oxidative damage in C. demersum. At 100-300 μg/L FLC, peroxidase (POD) and superoxide dismutase (SOD) were activated to scavenge free radicals in L. minor, while POD acted as a protective enzyme in C. demersum. At higher concentrations of FLC (≥ 1000-2000 μg/L), L. minor reached less than healthy stability through the regulation of the antioxidant enzyme system and the chlorophyll a/b value. POD, SOD, and protein content returned to normal levels, and the growth parameters increased. However, in C. demersum, the enzymes POD and SOD and soluble protein were damaged, and oxidative stress reached the highest level at 1000-2000 μg/L FLC. Taken together, our results suggested that when treated with FLC, L. minor was more sensitive at lower doses (20 μg/L) and more adaptive at higher doses (1000-2000 μg/L) than C. demersum.