Biology subjects

Lindermayr, C.

Publications and source records attributed to Lindermayr, C..

5 recordsLinked to original sources

bioRxiv2026

GSNOR-dependent nitric oxide homeostasis promotes recovery from repeated climate stress across generations in Arabidopsis thaliana

Climate change exposes plants to recurrent and interacting stresses, yet the extent to which these effects persist across generations, and the mechanisms involved, remain unclear. We propagated Arabidopsis thaliana wild type (WT, Col-0) and nitric oxide homeostasis mutant gsnor1-3 (hereafter, gsnor-ko) for five successive generations. Plants were grown under control, drought, elevated CO2, O3, warm temperature, and combined treatment scenarios for the first three generations (G1-G3), followed by two recovery generations under control conditions (G4-G5). We quantified rosette growth, photosynthetic traits, seed production, and transcriptome dynamics by RNA-seq. Across environments, gsnor-ko showed reduced vegetative growth and reproductive output relative to WT. Transcriptomic responses were strongly scenario- and generation-dependent, with the largest differential expression shifts observed under warm-climate and combined-treatment conditions. Compared with WT, gsnor-ko displayed broader gene overlap across generations and stronger retention or reconfiguration of stress-responsive states after stress withdrawal. Functional enrichment and candidate-gene analyses identified pathways/components linked to DNA methylation, heterochromatin maintenance, histone ubiquitination, m6A RNA regulation, and methyl-donor metabolism. Together, these results support a model in which GSNOR activity promotes transcriptomic recovery after repeated climate stress, whereas impaired GSNOR function shifts responses toward multi-generational persistence and epigenetically associated regulatory reconfiguration. HighlightGSNOR-dependent nitric oxide homeostasis promotes transcriptomic resetting after repeated climate stress, whereas impaired NO homeostasis favours multigenerational persistence and chromatin- and RNA-linked regulatory reconfiguration. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/742973v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@6031c6org.highwire.dtl.DTLVardef@163be5borg.highwire.dtl.DTLVardef@1665e9eorg.highwire.dtl.DTLVardef@1cde833_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2025

Threshold-like transcriptomic responses of European beech to simulated future climates

Beech (Fagus sylvatica) is one of the most important forest tree species in Europe, both in terms of land coverage and ecosystem services. Although it is projected to be strongly affected by climate change, insights into its functional genomic responses to realistic future scenarios are still lacking. We conducted a fully controlled ecotron experiment to examine the transcriptomic responses of 125 young, naturally regenerated beech trees exposed to regionalized dynamic climate series representing a reference period (1987-2016) and two future climate scenarios (Representative Concentration Pathways, RCP2.6 and RCP8.5, for 2071-2100) in Germany. RCPs describe alternative greenhouse gas trajectories established by the IPCC, ranging from strong mitigation (RCP2.6) to high, unmitigated emissions (RCP8.5), the latter representing a worst-case future scenario. Although both scenarios produced substantial transcriptional changes relative to the reference period, RCP8.5 elicited markedly stronger responses than RCP2.6, with nearly twice as many differentially expressed genes and unique transcriptional programs across functional categories that were not predictable from the RCP2.6 transcriptomes. Our study reveals emergent functional responses in European beech under projected late 21st-century climate conditions in Germany and highlights potential biomarkers for monitoring ecosystem responses to climate change.

ecology↗

bioRxiv2025

DNA methylome responses to biotic and abiotic stress in Arabidopsis thaliana: A multi-study analysis

Plants have evolved complex physiological and morphological strategies to cope with biotic and abiotic stress. At the molecular level, these responses are partly mediated by epigenetic mechanisms such as DNA methylation. In Arabidopsis thaliana, numerous studies have examined stress-induced changes in DNA methylation, aiming to elucidate their roles in stress acclimation. However, comparing these studies remains difficult due to variations in analytical methods and focus. To address this, we conducted an integrative analysis of 13 studies (16 datasets) using a unified bioinformatic pipeline to identify common and stress-specific methylation responses. Our results show that the number and distribution of differentially methylated regions (DMRs) vary by stress type and methylation context CG, CHG, and CHH. CG DMRs were primarily located in gene bodies, while CHG and CHH DMRs were enriched in transposable elements (TEs). Gene Ontology analysis revealed consistently enriched stress-related terms across conditions, indicating shared epigenetic regulation. As TEs have been proposed to act as stress sensors and regulators of nearby gene expression, we examined gene-proximal TEs in more detail. We found significant enrichment of stress-responsive methylation changes in LINE/L1, RathE1_ons, and DNA/HAT elements. While stress-induced methylation is often considered transient, many affected CG DMRs overlapped with loci known to accumulate stable epimutations over generations, suggesting that stress may contribute to long-term heritable epigenetic variation. These findings enhance our understanding of epigenetic regulation in plant stress responses, highlighting both shared and stress-specific methylation dynamics. Significance statementWe combined 16 Arabidopsis thaliana Whole-Genome Bisulfite Sequencing datasets to reveal common and stress-specific DNA methylation responses. Although global methylation levels remained stable, specific DMRs varied according to the type of stress and genomics context. Gene Ontology analysis revealed shared stress pathways. Gene-proximal transposable elements (TEs) (e.g. LINE/L1, RathE1_ons, DNA/HAT) were enriched for stress-responsive methylation changes. Notably, a subset of stress-induced CG DMRs overlap with epimutation-prone loci, suggesting an environmental route toward stable, heritable epigenetic variation.

plant biology↗

bioRxiv2020

Cyanobacterial NOS expression improves nitrogen use efficiency, nitrogen-deficiency tolerance and yield in Arabidopsis

Developing strategies to improve nitrogen (N) use efficiency (NUE) in plants is a challenge to reduce environmental problems linked to over-fertilization. The nitric oxide synthase (NOS) enzyme from the cyanobacteria Synechococcus PCC 7335 (SyNOS) has been recently identified and characterized. SyNOS catalyzes the conversion of arginine to citrulline and nitric oxide (NO), and then 70% of the produced NO is rapidly oxidized to nitrate by an unusual globin domain in its 5'-terminus. In this study, we assessed whether SyNOS expression in plants affects N metabolism improving NUE and yield. Our results showed that transgenic Arabidopsis plants had higher primary shoot length and shoot branching when grown in N-deficient conditions and higher seed production in N-sufficient and -deficient conditions. Moreover, transgenic plants showed significantly increased NUE in both N conditions. No differences were observed in N uptake for SyNOS lines. However, SyNOS lines presented an increase in N assimilation/remobilization under low N conditions. In addition, SyNOS lines had greater N-deficiency tolerance compared to wt plants. Our results support that SyNOS expression generates a positive effect on N metabolism and seed production in Arabidopsis, and it might be envisaged as a strategy to improve productivity in crops under adverse N environments.

plant biology↗

bioRxiv2020

Nitric oxide coordinates histone acetylation and expression of genes involved in growth/development and stress response

Nitric oxide (NO) is a signaling molecule with multiple regulatory functions in plant physiology and stress response. Besides direct effects on the transcriptional machinery, NO can fulfill its signaling function via epigenetic mechanisms. We report that light intensity-dependent changes in NO correlate with changes in global histone acetylation (H3, H3K9 and H3K9/K14) in Arabidopsis thaliana wild-type leaves and that this correlation depends on S-nitrosoglutathione reductase and histone deacetylase 6. The activity of histone deacetylase 6 was sensitive to NO, which demonstrates that NO participates in regulation of histone acetylation. ChIP-seq and RNA-seq analyses revealed that NO is involved in the metabolic switch from growth and development to stress response. This coordinating function of NO might be of special importance in adaptation to a changing environment and could therefore be a promising starting point to mitigating the negative effects of climate change on plant productivity.

plant biology↗