Networks of clocks and senescence and their transition in plant aging
We previously revealed that ORE1, a NAC transcription factor, forms a trifurcate feed-forward loop that regulates age-dependent cell death. We built time-evolving regulatory networks of NAC transcriptional factors, which show a regulatory inversion from activating to repressive regulatory modes at a pre-senescent transition stage. The inversion was governed by three hub NACs, and the mutants of hub NACs conferred earlier aging. Transcriptomic and proteomic approaches to NACs provide the structure of the regulatory network modules, utilized to negatively control senescence-promoting processes at the leaf transition stage and thus control the timing of age-dependent senescence.
Two rice subspecies, Indica and Japonica, show drastically different senescence. We found that a quantitative trait locus (QTL) on chromosome 9 is responsible for the short lifespan of Indica. The promoter of the Stay Green (SGR) in the QTL locus induces earlier and higher expression of the gene in Indica. The Japonica SGR allele introduced into Indica varieties led to delayed leaf senescence and increased productivity, suggesting OsSGR can be utilized in breeding to improve yield potential.
The circadian clock coordinates physiological processes with daily environmental cycles to enhance the fitness of organisms. To investigate the relationship between clock and aging in plants, we first analyzed potential role of circadian clock in regulating plant leaf aging. Among core clock components, PRR9 makes new-trifurcate feedforward loop for regulating leaf senescence with ORE1 and miR164. Conversely, we found circadian period length is shortened with leaf aging and clock-controlled ORE1 affects this period shortening by interacting with TOC1, a clock regulator.
Leaf senescence is regulated by diverse environmental factors. The red to far-red light ratio (R:FR) is reduced under vegetation shade, thus initiating leaf senescence. We revealed the antagonistic role of phyA and phyB in regulating leaf senescence under FR. Furthermore, we elucidated that the role of phyB in leaf senescence is changed by R:FR. These imply that antagonism between phyA and phyB is involved in fine-tuning leaf senescence under varying FR conditions.
Making sense and use of senescence
Leaf senescence limits yields in agronomic crops, biomass accumulation in forests, and shelf life of many horticultural crops. A senescing leaf becomes vulnerable to pathogen attack and many pathogens are fungi that may produce toxins, rendering food and feed unsafe. Research in my group has focused on (1) making sense of senescence at the molecular genetics and epigenetic levels. Briefly, we have employed various approaches to the molecular understanding of plant senescence, these include enhancer trap, transcriptome, epigenetics, and bioinformatics. We have identified numerous senescence-associated genes (SAGs) with a focus on genes encoding for transcription factors and genes involved in signal transduction. We have revealed an ABA-AtNAP transcription factor-SAG113 protein phosphatase C-SAG114 kinase regulatory chain, we have also identified recently duplicated transcription factor SAGs that mediate UV-induced senescence. (2) On making use of senescence, we have translated our above basic findings into practical applications for agricultural improvement. We have discovered that using CRIPR/CAS9 system to knock out senescence master regulator in crops can make the crops much more resistant to multiple abiotic stresses such as drought, salt, high temperature, cold, shade and UV. We are especially excited about the UV resistance. For example, lettuce in US and Canada has been repeatedly contaminated by dangerous E. coli strains. One easy way to address the contamination is to use UV to sterilize the lettuce. However, UV readily induces senescence. By using our molecular breeding strategy, we will be able to produce UV-resistant lettuce for consumers. This presentation will review and summarize the two aspects of our researches on plant senescence.
Autophagy, the master of bulk and selective recycling
Autophagy-mediated turnover plays an essential role in cellular homeostasis by removing damaged organelles and unwanted cytoplasmic constituents, and is critical for plant defense and robust nutrient recycling, especially during nitrogen and fixed-carbon starvation and senescence. This ‘self eating’ is mediated by a conjugation system that modifies a pair of ubiquitin-fold proteins ATG12 and ATG8 to eventually form an autophagic vesicle coated with the ATG8-phosphatidylethanolamine (PE) adduct. ATG8-PE serves two purposes, one is to help shape the encapsulating vesicles and their subsequent fusion with the vacuole, and the other is to provide a docking platform for a suite of ATG8-interacting proteins that selectively tether appropriate cargo to the membrane surface before enclosure. In addition to bulk degradation, the ATG8 system is responsible for clearing organelles like mitochondria (mitophagy), chloroplasts (chlorophagy) and peroxisomes (pexophagy), and large cytoplasmic complexes such as 26S proteasomes (proteaphagy) or ribosomes (ribophagy) when dysfunctional or no longer needed. Using a multi-omics approach with maize, we are attempting to understand how autophagy regulates the metabolome and sculpts the proteome during normal growth and during nutrient starvation. Surprisingly, broad alterations in the leaf metabolome were evident in plants missing the core autophagy component ATG12 even without stress, particularly affecting products of lipid turnover and secondary metabolites, which were underpinned by substantial changes in the transcriptome and/or proteome. Cross-comparison of mRNA and protein abundances allowed for the identification of organelles, protein complexes, and individual proteins targeted for selective autophagic clearance, and revealed several processes controlled by this catabolism. During our work selective proteaphagy, we discovered that ubiquitylation of dysfunctional complexes followed by their recognition by the autophagy receptor RPN10 are key to this clearance. Surprisingly, further studies on RPN10 revealed that it represents the founding member of a new class of autophagy adaptors/receptors that uses a UIM instead of an AIM sequence for binding to ATG8. Assays with candidate UIM proteins and non-biased screens revealed that these adaptors/receptors are likely present in all eukaryotes. One family of UBX-UIM proteins are of particular interest as they help direct the degradation of the AAA-ATPase CDC48/p97 hexamer that couples ATP hydrolysis to the extraction and removal of damaged proteins associated with ER stress. With this new class of adaptors/receptors, we greatly extend the reach of selective autophagy and potentially identify new factors regulating autophagic vesicle dynamics.
From genome to pan-genome in barley and wheat
Genomics based-breeding and research in molecular genetics and developmental biology was lagging behind in barley and wheat, two major crops in Europe and the world, because high quality genome sequences were missing. This has changed now, as for both species annotated high-quality reference chromosome-scale sequence assemblies were made available recently. In both cases the first reference sequence assemblies are representing a big leap forward, however, these assemblies are by far not representative for all domesticated genome diversity in both species. Thus in order to efficiently unlock genomic diversity for research and breeding, international efforts were initiated to describe the pan-genomes of barley and bread wheat by producing multiple high quality chromosome-scale assemblies. In addition, entire diversity collections of wheat and barley comprising several ten thousands of accessions are currently being genotyped by sequence-based methods. The presentation will report on the status of this research in the small grain cereals and provide detailed insights into the level of genome diversity of these major crop species.
Flooding stress survival: anticipate, acclimate and reanimate!
There has been a worldwide increase in intense precipitation events leading to floods. This trend exacerbated by global warming, is expected to persist in the future. Due to the extreme sensitivity of major crops to wet conditions, flooding poses a significant threat to food security. As a result of severely compromised gas exchange in an aqueous environment, flooded plants cannot sustain normal functioning. Flooding is a compound stress involving dynamic changes in oxygen, ethylene, reactive oxygen species and carbohydrates. The spatial and temporal dynamics of these signalling molecules convey important information about the nature of a flooding event and triggers crucial downstream acclimative responses. A comprehensive understanding of the hierarchy and function of these signals, their interaction and the changes they trigger to prolong plant survival in flooded conditions is vital for identifying tolerance strategies. In nature there is a tremendous variation in flooding tolerance both within and across species. This variation can be exploited to identify regulatory genes and networks mediating tolerance and provide possibilities towards improving flood tolerance of sensitive plant varieties. To this end, we have exploited natural variation in wild and model plant species, combining submergence physiology with genome-wide transcriptome and metabolite profiling. In this talk I will illustrate how we have utilised natural variation to unravel the molecular tapestry of flooding responses in plants and the genes and processes that determine the capacity for prolonged survival in flooded conditions.
Nitrogen recycling and mobilisation during leaf senescence.
Processes allowing the recycling of organic nitrogen and export to young leaves and seeds are important determinants of plant yield, especially when plants are nitrate limited. Mechanisms involved in the release of organic nitrogen from senescing leaves for remobilization include autophagy and proteolysis processes, amino acid interconversions, amino acid transports and phloem loading. Because autophagy, glutamine synthetase and asparagine synthetase genes are induced during leaf senescence and in response to nitrogen starvation, we investigated their roles in nitrogen remobilization efficiency. Using 15NO3– labeling at vegetative stage and following N remobilization in a pulse chase experiment, Arabidopsis mutants were analysed to identify the candidates playing a role in the 15N partitioning to the seeds at harvest (1;2). Their respective contributions will be summarized in order to give an overview of all the factors contributing to nitrogen remobilization during leaf senescence.
1. Masclaux-Daubresse C, Chardon F (2011) Exploring nitrogen remobilization for seed filling using natural variation in Arabidopsis thaliana. Journal of Experimental Botany 62: 2131-2142.
2. Guiboileau A, Yoshimoto K, Soulay F, Bataillé M, Avice J, et al. (2012) Autophagy machinery controls nitrogen remobilization at the whole-plant level under both limiting and ample nitrate conditions in Arabidopsis. New Phytologist 194: 732-740.
Integrative regulation of plant senescence by an EBFs-EIN3 module
Leaf senescence is a highly coordinated, complicated process involving the integration of numerous internal and environmental signals. The plant gas hormone ethylene is a well-known inducer of senescence, including fruit ripening and flower and leaf senescence. As the master transcription factor in ethylene signaling pathway, EIN3 functions as a positive regulator of leaf senescence via regulating multiple downstream target genes, such as miR164 and WRKY75. Recently, we found that an increase in endogenous spermidine through overexpression of spermidine synthase (SPDS) or the exogenous application of spermidine delays leaf senescence by promoting the protein degradation of ETHYLENE INSENSITIVE3 (EIN3) through stabilizing the EIN3 BINDING F-BOX1 (EBF1) and EBF2. Furthermore, the early senescence phenotypes of the spds1spds2 loss-of-function mutant was repressed by ein3eil1 double mutants or overexpression of EBF1/2 that function as negative regulators of leaf senescence. Our results suggest that spermidine could act as an anti-aging signal molecular to antagonize aging pathway in both animals and plants, and plants evolve a unique way to control the aging process via finely regulating the EBFs-EIN3 signaling cascade.
KIRA1 and ORESARA1 terminate flower receptivity by promoting senescence-induced programmed cell death in the Arabidopsis stigma
Flowers have a species-specific functional life span that determines the time frame in which pollination, fertilization, and seed set can successfully occur. The tissue of the floral stigma plays a key role in flower receptivity serving to intercept pollen and initiate pollen tube growth towards the ovary. Here we show that a tightly controlled age-induced programmed cell death process terminates the functional life span of the non-pollinated stigmatic papilla cells in Arabidopsis thaliana. We identified the leaf senescence regulator ORESARA1/ANAC092 and the previously uncharacterized KIRA1/ANAC074 as partially redundant key transcription factors that regulate stigma life span by directly controlling the expression of cell-death associated genes. KIRA1 expression is sufficient to induce programmed cell death and effectively terminate floral receptivity, while lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, however, the extension of stigma life span causes only a moderate extension of flower receptivity, suggesting that next to the stigma cell death program, other stigma-expressed pathways participate in the control of the flower’s receptive life span.
Systems biology of leaf ontogenesis in tobacco – from thylakoid biogenesis to senescence
The composition of the photosynthetic apparatus of higher plants is dynamically adjusted to long-term changes in the metabolic demand for ATP and NADPH imposed by stresses and leaf development. By changing photosynthetic complex stoichiometry, an imbalance between the photosynthetic production of ATP and NADPH and their metabolic consumption is avoided, and cytotoxic side reactions are minimized. We systematically compared the acclimation capacity of developing, mature and senescing leaves of tobacco to changing environmental conditions. Different to young developing leaves, the capacity of mature and senescing leaves to acclimate is very limited, because their photosynthetic complex biogenesis is massively repressed. This is possible because the cytochrome b6f complex, photosystem I and chloroplast ATP synthase are highly stable. They are only synthesized in young leaves, and under most conditions, their biogenesis is inactivated once the photosynthetic apparatus is fully established. Also strong reductions in chloroplast ribosome abundance restrict complex biogenesis in mature leaves. The residual ribosomes are largely required to sustain the repair of photosystem II, which has a much higher turnover than the other photosynthetic complexes. To gain more insights into the molecular basis of the repressed photosynthetic complex biogenesis in mature and senescing leaves, we performed a system-biology analysis of changes in photosynthetic complex accumulation, electron transport and leaf assimilation, chloroplast structure, and gene expression in both nucleus and chloroplast during the entire leaf ontogenesis of tobacco. Also metabolite profiles were generated. These data now enable us to gain detailed insights not only into the mechanisms controlling complex accumulation during leaf ontogenesis, but also to determine the underlying cellular and systemic signals.
Autophagy and Nutrient Remobilization during Senescence
Plants have the advantage of being able to produce their energy source by fixing carbon from the air through photosynthesis. However, under some conditions, such as during the development of non-photosynthetic tissues, senescence or abiotic stress, in which photosynthesis is downregulated, there is a shortage in carbon supply. Therefore, other resources must be used to meet the plant’s energy demands. Nutrient supply is thus, at least partially, met by the degradation of cellular components, resulting in pronounced metabolic changes.
Autophagy is a conserved eukaryotic process for the degradation of cellular constituents in the lytic compartment (vacuole in yeast and plants and lysosome in animals). The targets of autophagy are diverse and include soluble proteins, protein aggregates, whole organelles, and lipids. The autophagy mechanism is highly conserved, and homologs of many autophagy-related (ATG) genes have been characterized in plants, including the model plant Arabidopsis thaliana and the crop plant tomato (Solanum lycopersicum). The hallmark phenotype of autophagy-related mutants (atg mutants) is higher sensitivity nutrient starvation, early senescence, and lower yield. However, the direct impact of autophagy on cellular metabolism has not been well studied.
Our group studies nutrient remobilization in plants, focusing on autophagy as a model system for this process, by investigating the role of autophagy during different stages in plant life in which nutrient remobilization is crucial. We specifically focus on carbon starvation and fruit development in Arabidopsis and tomato, both accompanied by senescence. We observed distinct morphological differences between WT and atg mutant plants suggesting delayed growth and early senescence. We employed high-throughput metabolomic, lipidomic and proteomic analyses as well as extensive flux analyses, in order to elucidate the underlying causes of the morphological phenotype. We were able to show that autophagy has a global effect on central metabolism under conditions in which nutrient remobilization is necessary.
New insights into the molecular control of postharvest senescence through study of Arabidopsis inflorescences
Energy deprivation, wounding and disruption of water and nutrient supply are stresses that have the potential to cause the early deterioration of detached chlorophyllous tissues held in the dark. To identify the key stress signalling biology responsible for the precocious senescence of harvested tissues we developed a simple assessment system based on the degreening of detached dark-held immature Arabidopsis inflorescences. Using this system in combination with transcriptome profiling and forward and reverse genetics approaches we found that carbon deprivation-mediated metabolic reprogramming is a large part of the postharvest response. There is also a complex additive interplay between the major hormonal pathways and the progression of senescence. As found for other biological transitions, our most recent results suggest that postharvest deterioration may require a change in tissue competency before it can be initiated, which is governed by particular transcription factors. Our results, together with those of other researchers, also suggest that the same key regulators that control dark-mediated senescence in a detached system drive other major developmental programmes, including age-related leaf senescence, fruit ripening and stress response. Thus it will be argued that study of ‘artificial’ detached systems can be the most efficient route to understanding the key biology behind these diverse fundamentally important programmes.
Multidimensional approaches toward understanding leaf senescence: from omics to ecology
Leaf senescence is finely regulated and occurs by an intricate integration of multiple developmental and environmental signals. As a consequence, it is assumed that leaf senescence is a highly complex process involving the collective actions of thousands of genes and multiple pathways associated with aging, as well as their interplays, thereby complicating genetic and molecular analyses of senescence.
To understand leaf senescence, where the influence of many external and internal signals is balanced to allow controlled degeneration of cellular components, it is essential to study the system in its entirety. A highly resolved and multidimensional transcriptome map generated from our RNA-seq data revealed that senescing leaves showed more coordinated temporal changes in transcriptomes than growing leaves, with sophisticated regulatory networks comprising transcription factors and diverse small regulatory RNAs. Furthermore, we also performed comparative transcriptome analyses in genetic mutants, the ethylene-insensitive mutant ein2/ore3 and the constitutive cytokinin response mutant ahk3/ore12, to dissect the role of hormone signaling pathways during leaf senescence. From this study, we found that ethylene acts as a senescence-promoting factor via the transcriptional regulation of stress-related responses, whereas cytokinin acts as an anti-senescing agent by maintaining cellular activities and preserving the translational machinery.
Recently, we have developed a new approach and concept that will facilitate systemic biological understanding of leaf lifespan and senescence, utilizing the phenome high-throughput investigator (PHI) with a single-leaf-basis phenotyping platform. Our pilot tests showed empirical evidence for the feasibility of quantitative measurement of leaf senescence responses and improved performance in order to dissect the progression of senescence triggered by different senescence-inducing factors as well as genetic mutations. Such an establishment enables new perspectives to be proposed, which will be challenged for enhancing our fundamental understanding on the complex process of leaf senescence.
A suppressor of axillary meristem maturation promotes longevity in flowering plants
My lab has a long-standing history in studying the central role of the hormone auxin in plant development, with a specific focus on its polar transport and how abiotic signals alter plant development by changing the direction of this transport. More recently, my research interests have expanded to the role of auxin in plant developmental transitions or phase changes, such as the initiation of (somatic) embryogenesis and fruit development, and how these transitions mediate plant ageing.
In flowering plants, ageing is defined by a series of developmental transitions that starts with vegetative growth, and is followed by flowering, culminating in seed production. Tissue senescence and plant death follow seed production in monocarpic plants, while polycarpic plants prolong their life span by maintaining a number of vegetative axillary meristems, thereby allowing subsequent cycles of vegetative and reproductive development.
We identified a suppressor of axillary meristem maturation in Arabidopsis thaliana, with effects on plant shoot architecture and -longevity. Loss of suppressor function accelerated plant aging, whereas overexpression maintained vegetative axillary meristems and converted monocarpic A. thaliana and Nicotiana tabacum into (polycarpic) plants with reduced senescence, a prolonged life span and enhanced seed and biomass production. The position of this suppressor in the plant ageing pathway will be presented and discussed.
Chlorophyll catabolism precedes changes in chloroplast structure and proteome during leaf senescence.
The earliest visual changes of leaf senescence occur in the chloroplast as chlorophyll is degraded and photosynthesis declines. Yet, a comprehensive understanding of the sequence of catabolic events occurring in chloroplasts during natural leaf senescence is still missing. Here, we combined confocal and electron microscopy together with proteomics and biochemistry to follow structural and molecular changes during Arabidopsis leaf senescence. We observed that initiation of chlorophyll catabolism precedes other breakdown processes. Chloroplast size, stacking of thylakoids and efficiency of PSII remain stable until late stages of senescence, whereas the number and size of plastoglobules increase. Unlike catabolic enzymes, whose level increase, the level of most proteins decrease during senescence, and chloroplast proteins are overrepresented among these. However, the rate of their disappearance is variable, mostly uncoordinated and independent of their inherent stability during earlier developmental stages. Unexpectedly, degradation of chlorophyll-binding proteins lags behind chlorophyll catabolism. Autophagy and vacuole proteins are retained at relatively high levels, highlighting the role of extra-plastidic degradation processes especially in late stages of senescence. The observation that chlorophyll catabolism precedes all other catabolic events suggests that this process enables or signals further catabolic processes in chloroplasts and the entire senescing cells.
Social activity and conference dinner
Evening of Wednesday, 3rd April 2019