Czechia

After recovery from stress by pests and diseases, plants maintain an elevated state of defence. This induced resistance (IR) is often based on defence priming, which enables a faster and stronger immune response upon recurrent exposure to the same type of attacker. We study the epigenetic basis of this form of immune memory. We have recently shown that exposure of seedlings to herbivory induces long-lasting DNA de-methylation at transposable elements (TEs), which prime genomically distant defence genes. Although more variable in intensity, immune memory can partially be transmitted to the offspring of stressed plants. This heritable IR is proportional to the stress encountered in previous generations and involves the DNA demethylase ROS1. To advance our understanding of how DNA demethylation controls immune memory, we are following artificial strategies to manipulate the plant methylome. Using epigenetic recombinant inbred lines (epiRILs), which share the same genetic (wild-type) background but vary in heritable DNA methylation of TE-rich regions, we have previously identified epialleles that prime defence gene expression and provide high levels of disease resistance without negative effects on plant growth. To translate this form of epigenetic disease resistance to crops, we are currently developing a new method to introduce dosed amounts of ROS1-dependent DNA hypo-methylation into plant genomes. This tool will not only allow us to induce long-lasting resistance against pests and diseases, but also explore the epigenetic mechanisms by which plants establish, maintain and reset immune memory.



SEB Conference 2024

Primed plants do not forget: epigenetic drivers of immune memory

dna methylation.

disease resistance

stress memory

priming

epigenetics

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How steeply metabolic rate scales with body mass has been investigated and debated for a century; however, little is known about scaling within the same individuals as they grow, let alone how environmental variability affects such ontogenetic scaling relationships. We quantified the ontogenetic (within-individual) scaling of metabolic and growth rates of juvenile rainbow trout (Oncorhynchus mykiss) at 10°C after different early-life temperature treatments: (1) 10°C throughout the experiment; (2) 14°C as eggs, then 10°C from hatching onwards; and (3) 10°C as eggs, then 14°C from hatching to completion of the yolk-sac stage, then back to 10°C (10°C being the optimal temperature and 14°C simulating an early-life warm-spell). The steepness (scaling exponent) of both metabolic and growth rate scaling varied significantly but modestly among individuals. No difference was found in the scaling of standard metabolic rate (SMR) between treatments, but maximum metabolic rate (MMR) and aerobic scope (AS) scaled shallower in the 14°C-yolk group, whereas growth rate scaled steeper in the 14°C-egg group. This shows that a warm-spell can have lasting and negative carryover effects on juvenile aerobic performance (MMR and AS) if warming occurs in the yolk-sac stage, and induce compensatory growth if warming occurs in the egg stage. Correlations between metabolic and growth scaling exponents for individual fish further indicated that compensatory growth did not come at the expense of an elevated SMR but traded off with MMR and AS. The specific ontogenetic timing of temperature variability thus affects ontogenetic scaling of metabolic and growth rates differently and independently.

Early-life temperature variability has life-stage-specific effects on later-life ontogenetic scaling of fish metabolic and growth rates

Birds can adaptively regulate body mass in response to the cost-benefit trade-off between risks of starvation and predation. Despite this, little is known about how birds actually monitor, detect, and interpret their body mass and the mechanisms employed to regulate or adjust body mass to match their current ecological conditions. Using zebra finches, we experimentally increased perceived mass via attachment of weighted backpacks and provided the birds with either ad libitum standard mixed-seed diet or supplementary high-fat to investigate (a) how birds assess their own body mass and (b) the mechanisms birds employ to adjust mass. In both experiments, independent of diet treatment, birds with backpacks rapidly lost mass and reduced overall activity, time spent in active behaviors and food intake. We found no evidence that mass loss was due to stress associated with backpack attachment - there was no difference in plasma corticosterone concentrations directly after rapid mass loss. We found evidence that birds likely interpret body mass via a physical mechanosensory pathway rather than a physiological pathway - rapid loss of mass was not linked to changes in plasma metabolites (glycerol or triglyceride concentrations). Our results suggest that the process of energy balance and mass regulation can involve a greater array of mechanisms than simply matching energy in (food consumed) to energy out. Zebra finches are able to force a negative energy balance through other, unidentified, mechanisms, even while maintaining high-fat dietary intake and reducing overall activity.

The enviable ability of zebra finches to get slim, even when eating a tasty high-fat diet

SETBP1 haploinsufficiency disorder (SETBP1-HD) is a rare human genetic disorder (currently only 131 known cases) that affects development —particularly neurodevelopment. Individuals carry a hemizygous deletion or LoF in the SETBP1 region, which results in insufficient production of SET binding protein 1. Typically, SET binding protein 1 alters histone methylation to regulate the expression of target genes. When SETBP1 expression is low, key developmental genes are underexpressed, leading to developmental delay phenotypes. Symptoms include childhood hypotonia, motor development delay, intellectual and learning disabilities, anxiety, autism spectrum disorder, and attention-deficit/hyperactivity disorder. The aim of this study is to establish whether zebrafish represent a useful biomedical model for SETBP1-HD. Specifically, we deleted a single copy of SETBP1 via CRISPR transgenesis to investigate whether zebrafish SETBP1 hemizygosity induces the behavioral syndromes characteristic of human patients. Social and cognitive behaviours were assessed through larval behavioural assays; including thigmotaxis, startle response, and light dark response. A zebrafish model of SETBP1-HD will increase pathophysiological understanding of the disease and help to determine the molecular underpinnings of disease-linked variants, including Schinzel-Giedion syndrome and leukemia. Zebrafish represent a great model for high-throughput drug screening, which means that our transgenic SETBP1-HD lines may aid in the screening and development of potential SETBP1-HD therapies.

Modelling SETBP1 Haploinsufficiency Disorder (SETBP1-HD) in Zebrafish (Danio rerio)

Laminarin, one of the main storage polysaccharides of brown algae and diatoms, was recently found to be an important molecule in the world’s oceans by accounting for up to 26 ± 17 % of the particulate organic carbon. While digestive enzymes breaking down laminarin (laminarinases) have been intensely studied in a number of adult marine invertebrates, data on larval stages remain scarce. Abundantly inhabiting kelp forests as ecosystem engineers, especially sea urchins are found in laminarin-rich areas, suggesting that laminarin digestion plays a significant role throughout their life cycle. Considering the high laminarin abundance in microalgae, i.e. the food source of echinoderm larvae, digestive degradation might be beneficial, if not crucial, not only in adult sea urchins but also for larval performance within plankton. 
To disentangle the ecological and physiological role of laminarin for sea urchin larvae we conducted perturbation experiments with different laminarin concentrations and food sources (laminarin-rich and -poor microalgae) to evaluate the impact onto larval nutrition and performance. We analyzed (I) growth, survival and settlement success, as well as (II) laminarinase activity and expression patterns during larval development of the painted sea urchin Lytechinus pictus in response to the feeding regimes. 
The results contribute to a better understanding of laminarin dependent digestive dynamics in the early life stages of echinoderms, potentially affecting the recruitment of these important ecosystem engineers. 


Sea urchin larval digestion - the role of laminarin for larval fitness

Human activities represent one of the most dramatic forms of environmental change, affecting global biodiversity. Anthropogenic noise has increased in the last century with detrimental effects for wildlife on both individual and population levels. Sound pollution can compromise animal heath by imposing chronic stress and damaging the auditory system, affect intra- and inter specific relationships by disrupting communication and masking the presence of predators.
Shrews produce high-pitched laryngeal calls (“twittering calls”), with unclear function. It has been suggested as rudimentary echo-orientation mechanism, communication, or response to stressful stimuli. In this study, we analysed greater white-toothed shrews (Crocidura russula), trapped along a gradient of anthropogenic noise with the goal to link twittering calls to exposure to environmental stressors, through the analysis of faecal glucocorticoid levels. We hypothesize that animals inhabiting noisier locations would experience higher levels of stress, produce more twittering calls, and reduce exploratory behaviour to balance stress demands.
We live trapped 25 shrews in 6 locations with different sound patterns and maintained them in captivity for 5 consecutive days, for repeated measurement of twittering calls, exploratory behaviour, and stress levels.
Results show that variation in noise levels influences the shrews’ stress response, independently of the average noise levels. Neither average noise levels nor its variation induced a change of vocalisations. While time in captivity resulted in a reduction of exploratory behaviour and twittering calls, we did not find evidence supporting a link between stress levels and twittering calls.


Noisy places, noisy animals? - Shrew responses to sound pollution

As Journal of Experimental Botany (JXB) editors, we often receive manuscripts focusing on phenotyping drought tolerance and plant responses to water deficit. Despite extensive research identifying multiple drought tolerance genes in recent decades, practical field application remains limited. We have observed that the quality of research in this field frequently suffers from flawed experimental designs, inconsistent terminology, overinterpretation of data, or unrealistic lab-to-field extrapolations. To tackle these challenges, the JXB editorial board established a working group to guide better experiment design, data interpretation, and result reporting, focusing on experiments performed in supposedly ‘controlled conditions’. Our recommendations include:
• Establishing clear, testable hypotheses and objectives moving away from vague goals like "improving drought tolerance".
• Utilizing precise, consensus-driven terminology to clearly communicate objectives and hypotheses. 
• Designing experiments that adequately account for the complexities of genotype-environment (GxE) interactions, by including sufficient biological replicates and conducting multiple experiments as well as measuring soil, plant and environmental parameters in parallel to monitor complex cross-interactions. 
• Considering the impact of whole-plant transpiration on soil-moisture and stress levels, stemming from interactions with pot sizes and soil-substrate, and acknowledging that plant responses to drought depend on, and also affect, their developmental stage.
These guidelines aim to enhance research quality, contributing vital knowledge to combat the growing threat of drought to agriculture.


Guidelines for designing and interpreting drought experiments in controlled conditions 

The development of multicellular organisms requires the integration of signals controlling and coordinating cell fates. This process relies on numerous regulatory events that impact both chromatin structure and transcription. Chromatin undergoes global modifications at specific times and within specific cell subsets to dictate distinct cellular programs. However, the mechanisms by which chromatin is modulated during development remains highly elusive.
Plants are ideal models for investigating cell-specific chromatin remodelling. Plant cells do not move, and their plastic development is the result of an exquisite interaction between environmental and intrinsic signals. How does this signal crosstalk guide chromatin orchestration?
Our findings, derived from the study of flowering time in Arabidopsis may bring some answers. One key function of the plant hormone Brassinosteroids is to regulate the vegetative to reproductive fate transition of the cells in flower primordium. BR signalling acts through inactivation of GSK3 kinases responsible for the modulation of other protein’s activity. Interestingly, in contrast to other hormones, BR do not undergo long distant transport. We discovered that the BR dependent GSK3s bind and phosphorylate a central component of chromatin machinery involved in establishing and maintaining transcriptional programs. This finding may help explaining how chromatin is orchestrated in specific cells to guide cell fate transitions. 


Chromatin Orchestration in Plant Development: Insights from Brassinosteroid Signaling and Flowering Time Control

Many fastidious (or unculturable) pathogens, such as the Candidatus Liberibacter spp. associated with citrus greening (HLB) disease pose an immense threat to crop production and cause billions of dollars in losses worldwide. Unlike studies of model plant-pathogen systems, studies of fastidious crop pathogens are greatly hindered due to the unculturable, obligate lifestyle of the pathogens and the relative recalcitrance of the host crops to conventional genetic and laboratory evaluation approaches. To overcome these bottlenecks, we developed an innovative plant hairy root-based efficacy testing system suitable for faster pre-screening of diverse resistance and susceptibility genes and small molecule-based antimicrobials. Using this approach, we identified multiple novel genes, antimicrobial peptides, and chemicals that showed efficacy against Candidatus Liberibacter spp. Ongoing field trials with selected candidates are promising, with improved crop yield and health. One or more of these solutions could be further deployed as products for crop disease management.

Novel strategies to screen and evaluate genetic- and chemical-based solutions for crop improvement

Plant Class I formins represent a unique family of cytoskeletal organizers that are at the same time integral membrane proteins. We have previously reported that the GFP fusion of the Arabidopsis formin AtFH1, which is considered to be the main housekeeping Class I formin expressed in majority of tissues according to the available gene expression data, also transiently localised to the tonoplast in the root transition zone at or around the time of major membrane rearrangements that generate the large central vacuole typical for differentiated plant cells (Oulehlová et al., 2019 – https://doi.org/10.1093/pcp/pcz102). It is currently unknown whether AtFH1 has an active role in tonoplast rearrangements or whether it transiently passes through the tonoplast while being sorted for vacuolar degradation. A newly prepared fusion of AtFH1 with a different, pH-insensitive fluorescent protein, as well as pharmacological treatment with concanamycin A, showed, in addition to known AtFH1-GFP localisation, also presence of AtFH1 within vacuolar lumen in the root elongation zone and mature tissues, supporting the degradation hypothesis. However, we also found quantitative, sometimes significant changes in vacuolar organization in mutants lacking AtFH1, using both established vacuolar morphology metrics and a newly developed method for quantitative evaluation of tonoplast topology, supporting a tonoplast-associated function of AtFH1. Therefore, depending on the exact developmental stage and conditions, both of the hypotheses may be correct.

The role of Arabidopsis Class I formin AtFH1 during vacuolar development – to use or to degrade?

Transposable Elements (TEs) are the major force in genome plasticity and gene evolution, with LTR retrotransposons (LTR-TEs) constituting the most abundant class. LTR-TEs are considered autonomous when they contain the coding sequence for the translation of all factors required for their replication and transposition, and nonautonomous if they require that such factors are provided in trans. While several autonomous LTR-TEs has been found mobile in Arabidopsis thaliana epigenetic mutants or epigenetic recombinant inbreed lines (epiRILs), non-autonomous LTR-TEs ha never observed mobile in real time experiments. In this study, we observe that the LTR_gypsy transposon ATGP2N mobilises in epiRILs and transpose with high specificity into ribosomal repeats. Notably, an identical homologous region is present in the LTRs of ATGP2N and the autonomous LTR-TE, suggesting that ATGP2N hijacks ATGP2 factors for its transposition. Our studies shed light on the transpositional dynamics of nonautonomous LTR elements and contribute to expanding our knowledge of LTR transposition mechanisms.

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Early-life temperature variability has life-stage-specific effects on later-life ontogenetic scaling of fish metabolic and growth rates

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Inducible and Targeted DNA Demethylation Reveal a Causal Role for Epigenetic Reprogramming in Plant Immune Memory

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