Biology subjects

Tarkowska, D.

Publications and source records attributed to Tarkowska, D..

9 recordsLinked to original sources

bioRxiv2025

INDETERMINATE DOMAIN-DELLA protein interactions orchestrate gibberellin-mediated cell elongation in wheat and barley

DELLA proteins, members of the GRAS-domain family of transcriptional regulators, are critical for plant growth and development. They modulate transcription indirectly via interactions with hundreds of transcription factors. The phytohormone gibberellin (GA) triggers DELLA degradation, providing a mechanism by which plants can integrate developmental and environmental signals to regulate gene expression and optimize growth responses. In agriculture, DELLA mutations have been instrumental in improving crop performance. Most modern wheat (Triticum aestivum L.) varieties carry Rht-B1b or Rht-D1b alleles that encode DELLA proteins resistant to GA-mediated degradation, resulting in constitutive partial suppression of stem growth, a semi-dwarf stature and lodging resistance. However, these alleles also reduce nitrogen use efficiency and early vigour, limiting their utility in some environments. Understanding how DELLA proteins regulate growth and development is, therefore, critical for refining breeding strategies. In this study, we identified the orthologous C2H2 zinc-finger transcription factors INDETERMINATE DOMAIN 5 (IDD5) in wheat and SEMI-DWARF 3 (SDW3) in barley (Hordeum vulgare) as positive regulators of stem and leaf expansion. Both IDD5 and SDW3 physically interact with, and act downstream of, DELLA proteins as key components of GA-mediated growth responses. Altered expression levels of GA biosynthesis genes suggest that IDD5 helps maintain GA homeostasis in addition to growth regulation. Loss-of-function mutations in IDD5 and SDW3 confer a GA-insensitive semi-dwarf phenotype comparable to that of the Rht-D1b Green Revolution allele, highlighting their potential as novel dwarfing alleles for cereal improvement. Significance statementOur study identifies homologous wheat and barley transcription factors (IDD5 and SDW3) that interact with DELLA proteins to regulate plant height. Unlike conventional Green Revolution DELLA mutations, which can reduce height but also have drawbacks such as lower nitrogen-use efficiency, these IDD genes may provide more targeted approaches to manage plant growth. By showing how IDD proteins promote stem and leaf expansion and by revealing their potential as alternative dwarfing alleles, our research opens new avenues both for fundamental research into plant growth pathways and for applications in cereal breeding. Ultimately, it could help produce crops with improved lodging resistance and fewer negative side effects than current dwarfing alleles.

plant biology↗

bioRxiv2025

Arabidopsis seed stored mRNAs and translation regulation during post-harvest ripening and imbibition.

Seed germination marks the critical transition from dormancy to active growth, driven by environmental cues and water availability. This study explores translational regulation during germination by comparing two Arabidopsis thaliana accessions with contrasting dormancy phenotypes: Columbia (Col), which germinates readily, and Cape Verde Islands (Cvi), which exhibits deep dormancy. Using sucrose gradient centrifugation, we isolated monosomal and polysomal fractions from freshly harvested (FH), after-ripened (AR), and imbibed (IM) seeds. RNA-seq analysis revealed stage- and genotype-specific gene expression, with Col IM seeds displaying the highest number of expressed genes. We identified [~]14,000 mRNAs in FH seeds, increasing to 19,000 in Col and 17,000 in Cvi upon imbibition. Of these, 9,000 were shared, while 3,000 were accession-specific in monosomes. Enrichment analysis highlighted molecular pathways associated with translation and dormancy release. Analysis of RNA modifications identified N1-methyladenosine (m1A) as the predominant modification, with Col seeds exhibiting higher m1A levels than Cvi, peaking at three months post-harvest. m6A sequencing revealed distinct modification patterns between accessions, with the highest abundance of m6A-modified transcripts in IM seeds. Positional analysis of m6A peaks suggested a link to differential gene expression between Col and Cvi. Proteomic analysis identified [~]15,000 proteins, with translation-related proteins enriched in IM seeds. Notable differences between Col and Cvi were observed in both monosomal and polysomal fractions. RNA-binding proteins exhibited similar profiles in FH and AR stages but diverged significantly in IM seeds. Col-specific proteins were enriched in 40S ribosomes, processing bodies, and RNA-binding complexes. These findings provide new insights into the molecular and translational dynamics underlying seed germination, advancing our understanding of dormancy release and early seedling establishment.

plant biology↗

bioRxiv2023

The dimorphic diaspore model Aethionema arabicum (Brassicaceae): Distinct molecular and morphological control of responses to parental and germination temperatures

Plants in habitats with unpredictable conditions are often characterized by diversifying their bet-hedging strategies that ensure fitness over a wider range of variable environmental factors. A striking example is the diaspore (seed and fruit) heteromorphism that evolved to maximize species survival in Aethionema arabicum (Brassicaceae) in which external and endogenous triggers allow the production of two distinct diaspores on the same plant. Using this dimorphic diaspore model, we identified contrasting molecular, biophysical, and ecophysiological mechanisms in the germination responses to different temperatures of the mucilaginous seeds (M+ seed morphs), the dispersed indehiscent fruits (IND fruit morphs), and the bare non-mucilaginous M- seeds obtained by pericarp (fruit coat) removal from IND fruits. Large-scale comparative transcriptome and hormone analyses of M+ seeds, IND fruits, and M- seeds provided comprehensive datasets for their distinct thermal responses. Morph-specific differences in co-expressed gene modules in seeds, as well as seed and pericarp hormone contents identified a role of the IND pericarp in imposing coat dormancy by generating hypoxia affecting ABA sensitivity. This involved expression of morph-specific transcription factors, hypoxia response and cell wall-remodeling genes, as well as altered abscisic acid (ABA) metabolism, transport, and signaling. Parental temperature affected ABA contents and ABA-related gene expression and altered IND pericarp biomechanical properties. Elucidating the molecular framework underlying the diaspore heteromorphism can provide insight into developmental responses to globally changing temperatures. IN A NUTSHELL BackgroundHeteromorphic diaspores (fruits and seeds) are an adaptive bet-hedging strategy to ensure survival in spatiotemporally variable environments. The stone cress Aethionema arabicum, an annual plant native to semi-arid habitats in Anatolia (Turkey), one of the worlds hotspots of biodiversity. It is a close relative of Arabidopsis, rapeseed, cabbage and other Brassica crops, but in contrast to these Ae. arabicum disperses two distinct diaspores from the same plant. These dimorphic diaspores are the mucilaginous seeds (dispersed by pod shatter) and indehiscent fruits (dispersed by abscission). The wing-like pericarp (fruit coat) of the single-seeded indehiscent fruit allows wind dispersal over large distances. The amounts and ratios of the dimorphic diaspores are variable and depend on the environmental conditions. The dimorphic diaspores differ in morphology, dormancy and germination properties and thereby make Ae. arabicum an excellent model for the comparative investigation of the underpinning molecular mechanisms. QuestionWe asked how temperature during fruit and seed formation and during seed germination affect dormancy release and germination speed, and how the morphology, hormonal regulation, and the expression of genes differ between the dimorphic diaspores. FindingsLarge-scale comparative transcriptome and hormone analyses of the mucilaginous seeds and the indehiscent fruits, as well as the seeds artificially extracted from indehiscent fruits by pericarp (fruit coat) removal, provided comprehensive datasets for their distinct thermal responses. Material obtained from plants grown at different temperatures during reproduction was imbibed at different temperatures for germination. This altered the abscisic acid (ABA) metabolism and the pericarp biomechanical properties. Diaspore-specific differences in response to distinct imbibition temperatures identified distinct gene expression patterns in seeds, distinct seed and pericarp hormone contents, and a role of the pericarp in generating hypoxia inside the fruit and imposing coat dormancy. This revealed distinct combinations of specific transcription factors, hypoxia responses and cell wall-remodeling genes, as well as altered signaling pathway genes. Next stepsOur large-scale comparative transcriptome datasets are easily and publicly accessible via the Aethionema arabicum web portal (https://plantcode.cup.uni-freiburg.de/aetar_db/index.php). We plan to expand this by future work on seedlings derived from the dimorphic diaspores, by comparing different Ae. arabicum genotypes, and by studying responses to specific stresses. Understanding the molecular basis of this fascinating example of developmental diversity and plasticity and its regulation by temperature is expected to add insight how plants respond to changing environmental conditions.

plant biology↗

bioRxiv2023

Cell wall integrity modulates a PHYTOCHROME-INTERACTING FACTOR (PIF) - HOOKLESS1 (HLS1) signalling module controlling apical hook formation in Arabidopsis.

Etiolated seedlings of dicots form an apical hook to protect the meristems during soil emergence. Hook formation is the result of differential growth on both sides of the hypocotyl apex and is tightly controlled by environmental cues and hormones, among which auxin and gibberellins (GAs) are the main contributors. Cell expansion is tightly regulated by the cell wall, but whether and how feedback from this structure contributes to hook development is still unclear. Here we show that etiolated seedlings of the Arabidopsis thaliana quasimodo2-1 (qua2) mutant, defective in pectin biosynthesis, display severe defects in apical hook formation and maintenance, accompanied by loss of asymmetric auxin maxima and differential cell expansion. Moreover, qua2 seedlings show reduced expression of HOOKLESS1 (HLS1) and PHYTOCHROME-INTERACTING FACTOR 4 and 5 (PIF4/5), positive regulators of hook formation, and accumulate reduced levels of the active gibberellin GA4. Treatment of wild-type seedlings with the cellulose inhibitor isoxaben (isx) also prevents hook development and represses HLS1 expression and PIF4 accumulation. Moreover, isx stabilizes the DELLA protein REPRESSOR OF ga1-3 (RGA), which inhibits HLS1 expression and hook formation. Exogenous GAs or HLS1 overexpression partially restore hook development in isx-treated seedlings. Notably, agar concentration in the medium restores, both in qua2 and isx-treated seedlings, hook development and WT-like levels of PIFs and HLS1. We propose that turgor-dependent signals link changes in cell wall integrity to the PIF4/5-HLS1 signalling module to repress differential cell elongation during hook formation. Significance statementCell wall integrity modulates apical hook development through poorly understood mechanisms. We show here that, in Arabidopsis, repression of hook formation by either mutations in pectin biosynthesis or by isoxaben treatment is at least partially mediated by the downregulation of a gibberellin-controlled signalling module that comprises PIF4/5 and HLS1. Our results indicate that the signals derived from changes in the cell wall can modulate hormone-mediated pathways to control asymmetric growth during plant development.

plant biology↗

bioRxiv2022

The Phosphate Deprivation Response is Mediated by an Interaction between Brassinosteroid Signaling and Zinc in Tomato

Phosphate is a necessary macronutrient for basic biological processes, plant growth, and agriculture. Plants modulate their root system architecture and cellular processes to adapt to phosphate deprivation albeit with a growth penalty. Excess application of phosphate fertilizer, on the other hand, leads to eutrophication and has a negative environmental impact. Moreover, phosphate mined from rock reserves is a finite and non-recyclable resource and its levels are nearing complete depletion. Here, we show that Solanum pennellii, a wild relative of tomato, is partially insensitive to phosphate deprivation. Furthermore, it mounts a constitutive response under phosphate sufficiency. We demonstrate that activated brassinosteroid signaling through a tomato BZR1 ortholog gives rise to the same constitutive phosphate deficiency response, which is dependent on zinc over-accumulation. Collectively, these results reveal an additional strategy by which plants can adapt to phosphate starvation.

plant biology↗

bioRxiv2022

Phytochromes mediate germination inhibition under red, far-red, and white light in Aethionema arabicum

The view on the role of light during seed germination stems mainly from studies with Arabidopsis, where light is required to initiate this process. In contrast, white light is a strong inhibitor of germination in other plants, exemplified by accessions of Aethionema arabicum, another Brassicaceae. Their seeds respond to light with gene expression changes of key regulators converse to Arabidopsis, resulting in antipodal hormone regulation and prevention of germination. The photoreceptors involved in this process in A. arabicum were unknown. Screening the first mutant collection of A. arabicum, we identified koy-1, a mutant that lost light inhibition of germination, due to a deletion in the promoter of HEME OXYGENASE 1, the gene for a key enzyme in the biosynthesis of the phytochrome chromophore. koy-1 seeds are unresponsive to red- and far-red light and hyposensitive under white light. Comparison of hormone and gene expression between wild type and koy- 1 revealed that very low light fluence stimulates germination, while high irradiance of red and far-red light is inhibitory, indicating a dual role of phytochromes in light-regulated seed germination. The mutation also affects the ratio between the two fruit morphs of A. arabicum, suggesting that light reception via phytochromes can fine-tune several parameters of propagation in adaptation to conditions in the habitat. One sentence summaryCharacterization of a phytochrome chromophore biosynthesis mutant demonstrates an active role of phytochromes in the light-inhibited seed germination in Aethionema arabicum.

plant biology↗

bioRxiv2021

Inhibition of gibberellin accumulation by water deficiency promotes fast and long-term 'drought avoidance' responses in tomato

Plants reduce transpiration to avoid dehydration during drought episodes by stomatal closure and inhibition of canopy growth. While abscisic acid (ABA) has a primary role in drought avoidance, previous studies suggest that gibberellin (GA), might also be involved. Here we show in tomato (Solanum lycopersicum) that shortage of water inhibited the expression of the GA biosynthesis genes GA20 oxidase1 (GA20ox1) and GA20ox2 and induced the GA-deactivating gene GA2ox7 in leaves and guard cells, resulting in reduced bioactive GA levels. Drought regulation of GA metabolism was mediated by ABA-dependent and independent pathways, and by the transcription factor DEHYDRATION RESPONSIVE ELEMENT BINDING (DREB), TINY1. Mutations in GA20ox1 and GA20ox2 reduced water loss due to the smaller canopy area. On the other hand, loss of GA2ox7 did not affect leaf size, but attenuated stomatal response to water deficiency; during soil dehydration, ga2ox7 plants closed their stomata and reduced transpiration later than WT, suggesting that ga2ox7 stomata are hyposensitive to soil dehydration. Together, the results suggest that drought-induced GA deactivation in guard cells contributes to stomatal closure at the early stages of soil dehydration, whereas inhibition of GA synthesis in leaves promotes mainly the long-term reduction in canopy growth to reduce transpiration area.

molecular biology↗

bioRxiv2021

An HB40 - JUNGBRUNNEN1 - GA 2-OXIDASE regulatory module for gibberellin homeostasis in Arabidopsis

The phytohormones gibberellins (GAs) play fundamental roles in almost every aspect of plant growth and development. Although there is good knowledge about GA biosynthetic and signaling pathways, factors contributing to the mechanisms homeostatically controlling GA levels remain largely unclear. Here, we demonstrate that homeobox transcription factor HB40 of the HD-Zip family in Arabidopsis thaliana regulates GA content at two additive control levels. We show that HB40 expression is induced by GA and in turn reduces the levels of endogenous bioactive GAs by a simultaneous reduction of GA biosynthesis and increased GA deactivation. Hence, HB40 overexpression leads to typical GA-deficiency traits, such as small rosettes, reduced plant height, delayed flowering, and male sterility. In contrast, a loss-of-function hb40 mutation enhances GA-controlled growth. Genome-wide RNA-sequencing combined with molecular-genetic analyses revealed that HB40 directly activates transcription of JUNGBRUNNEN1 (JUB1), a key TF repressing growth by suppressing GA biosynthesis and signaling. HB40 also represses genes encoding GA 2-oxidases (GA2oxs) which are major GA catabolic enzymes. The effect of HB40 is ultimately mediated through induction of nuclear growth-repressing DELLA proteins. Our results thus uncover an important role of the HB40/JUB1/GA2ox/DELLA network in controlling GA homeostasis during plant growth.

plant biology↗

bioRxiv2018

A novel model plant to study the light control of seed germination

Timing of seed germination is crucial for seed plants and coordinated by internal and external cues, reflecting adaptations to different habitats. Physiological and molecular studies with lettuce and Arabidopsis thaliana have documented a strict requirement for light to initiate germination and identified many receptors, signalling cascades, and hormonal control elements. In contrast, seed germination of several other plants is inhibited by light, but the molecular basis of this converse response is unknown. We describe Aethionema arabicum (Brassicaceae) as a suitable model plant to investigate the mechanism of germination inhibition by light, as it comprises accessions with natural variation between light-sensitive and light-neutral responses. Inhibition is independent of light wavelength and increases with light intensity and duration. Gibberellins and abscisic acid are involved in the control of germination as in Arabidopsis, but transcriptome comparisons of light- and dark-exposed Aethionema arabicum seeds revealed that expression of genes for key regulators upon light exposure undergo converse changes, resulting in antipodal hormone regulation. This illustrates that similar modular components of a pathway in light-inhibited, light-neutral and light requiring germination among the Brassicaceae have been assembled by evolution to produce divergent pathways, likely as adaptive traits.\n\nHighlightIn contrast to light requirement for Arabidopsis seed germination, germination of several Aethionema arabicum accessions is inhibited by light, due to antipodal transcriptional regulation of hormone balance.

plant biology↗