Biology subjects

Julkowska, M. M.

Publications and source records attributed to Julkowska, M. M..

14 recordsLinked to original sources

bioRxiv2026

The chloroplast CLP chaperone-protease system controls the steady-state abundance of the singlet oxygen sensors EXCUTER 1 and 2

O_LIThe chloroplast CLP chaperone-protease is essential for chloroplast biogenesis. CLP substrate selection is aided by the N-recognin CLPS1 and CLPF adaptors. They interact with each other and the CLPC1 chaperone, but their specific functions are poorly understood. C_LIO_LIWe employed in vivo CLPC1 substrate-trapping in Arabidopsis by expressing a 35S:CLPC1-TRAP-STREPII transgene in wild-type (WT), clpf, clps1, and clpfclps1 to test the consequences of the loss of these adaptors on CLPC1-trapped proteins. Immunoblotting and protein half-life experiments were carried out for identified CLP substrates. C_LIO_LIExpression of the 35S:CLPC1-TRAP-STREPII in clps1cpf was embryo lethal. CLPF was trapped at a reduced level in clps1, supporting CLPS-CLPF interactions. Chloroplast 1O2 sensor EXECUTER1 (EX1) was trapped in WT and clps1 but not significantly in clpf. Steady-state protein accumulation of EX1 and its homolog EX2 increased 30-fold in the CLPC1-TRAP lines and clpr2-1, but not in clpf or clps1. In planta experiments showed that the half-life of EX1 is [~]3-fold longer in clpc1-1 than in WT, but EX1 half-life was unaffected in clpf. C_LIO_LIWe conclude that the CLP system plays a key role in EX1,2 homeostasis by keeping their intra-chloroplast concentrations low through continuous degradation, upstream of their 1O2 signaling function. C_LI

plant biology↗

bioRxiv2026

Gravitropism Shapes the Pareto Front of Root System Architecture

The root systems of wild tomatoes (S. Pimpinellifolium) can be understood as biological networks in which the lateral roots branch from a single main root and together balance two competing objectives: minimizing the material cost of building the network (wiring cost) and minimizing the transport time from the root tips to the shoot (conduction delay). Our prior work showed that S. Pimpinellifolium root architectures cluster near the Pareto-optimal front defined by these two objectives, with morphological diversity resolving into four qualitative topologies ((Chandrasekhar and Julkowska, 2022)). That framework assumed lateral roots grow as straight lines - ignoring gradual onset of lateral root gravitropism, the tendency of roots to curve toward the gravity vector. Because curved trajectories are longer than straight lines, gravitropism directly increases both wiring cost and conduction delay, constraining which architectures are physically realizable and thereby reshaping the Pareto front itself. Here we extend the model to explicitly incorporate lateral root gravitropism, producing predicted architectures that align much more closely with observed S. Pimpinellifolium root systems. We present a computational method to infer gravitropic sensitivity directly from anatomical tracing data - without reorientation assays - and apply it to 2423 arbors across different root topologies, growth conditions, and hormone treatments. Incorporating gravitropism reveals variation invisible to the straight-line model:notably, lateral roots show reduced gravitropic sensitivity under salt stress, mirroring a phenomenon previously described only for main roots and overlooked in lateral roots until now.

plant biology↗

bioRxiv2025

Identification of molecular mechanisms contributing to acquired thermotolerance by transcriptome profiling

Heat stress poses a serious threat to plant survival and productivity, and has a direct influence on crop yield stability. Plants response to high temperature is tightly controlled by complex genetic networks. Plants can be acclimated through gradual pre-exposure to increasing temperatures and that in turn causes higher survival in subsequent and otherwise lethal heat stress conditions. To investigate the physiological and molecular processes underlying heat acclimation and recovery, we examined changes in Arabidopsis thaliana transcriptome throughout the acclimation and the subsequent heat shock treatment. Groups of differentially expressed genes and enriched biological pathways that constitute the heat transcriptional memory were identified. The function of flavonoids in plant heat stress were further explored experimentally. In addition, we observed altered stomata density and aperture responses in heat acclimated plants, and this might be partially controlled by AGAMOUS-LIKE16 (AGL16) transcription factor and its negative regulator microRNA824 (miR824).

plant biology↗

bioRxiv2025

Exogenous Hormone Treatments Reveal Species-Specific Regulation of Individual Components of Root Architecture and Salt Ion Accumulation in Cultivated and Wild Tomatoes

Hormonal signaling shapes plant architecture and salt stress responses, but its effects on root architecture and ion accumulation remain unclear. Here, we conducted a detailed analysis of how individual hormone treatments affect root architecture and ion accumulation under salt stress in tomato. The study focused on three tomato accessions with varying responses to salt stress. Our findings revealed distinct, species-specific hormonal effects. Auxin, ethylene, and gibberellin promoted lateral root development, yet their impacts on ion accumulation, particularly in Na/K ratio, varied considerably. To explore the molecular basis of these differences, we examined Arabidopsis mutants for ethylene- and auxin-related genes, revealing novel components of hormone signaling involved in the salt stress response. Further, analysis of tomato mutants with impaired ethylene perception demonstrated that the nr mutant exhibits increased root growth and a higher shoot Na/K ratio, largely due to reduced K retention. Our integrated physiological and genetic analysis reveals species-specific hormonal strategies can boost crop performance under salt stress.

plant biology↗

bioRxiv2024

Root Remodeling Mechanisms and Salt Tolerance Trade-Offs: The Roles of HKT1, TMAC2, and TIP2;2 in Arabidopsis

Plant responses to salt stress involve complex processes integrating short- and long-term adaptations, including changes in ion transport, systemic signaling, root architecture, and biomass distribution. A key adaptive mechanism involves the regulation of sodium (Na+) and potassium (K+) ion transport via Class 1 HKT1 transporters, which reduce Na+ accumulation in shoots, thereby enhancing salinity tolerance but at the expense of lateral root development. In this study, we identified differential roles of TMAC2 in modulating ABA accumulation and lateral root development under salt stress in two distinct Arabidopsis genotypes, Col-0 and C24. Overexpression of TMAC2 in the Col-0 background increased ABA accumulation, resulting in reduced lateral root development, suggesting a positive feedback loop involving HKT1, TMAC2, and ABA signaling. In contrast, TMAC2 overexpression in C24 reduced ABA accumulation in lines overexpressing HKT1, indicating genotype-specific differences in the TMAC2-HKT1 interaction. Additionally, we observed that the co-expression of TMAC2 and HKT1 in Col-0 induced ABI4 and ABI5 transcription factors, which are known to mediate salt sensitivity. These findings reveal a regulatory network where TMAC2 and HKT1 modulate salt stress responses through genotype-dependent feedback mechanisms. Our results highlight the complexity of root remodeling under salt stress and the crucial role of genetic background in shaping these adaptive responses.

plant biology↗

bioRxiv2024

Dissecting the genetic regulation of lateral root development in tomato under salt stress

Roots are the primary site for sensing salt, making them critical to understanding how plants adapt to salinity. Unraveling the genetic and molecular mechanisms that maintain root growth under salt stress is essential for developing resilient crops. Tomatoes are vulnerable to salinity, as over 50% of arable land is projected to become saline by 2050. While salt stress effects on tomato seed germination, shoot growth, and fruit yield are well-documented, the genetic basis of root development under salinity remains underexplored. Previous studies focused on physiological responses of roots in a narrow range of cultivated-tomatoes, overlooking the genetic diversity for salt resilience in wild-relatives like Solanum pimpinellifolium. Here, we investigated salt-induced changes in root system architecture (RSA) across a natural diversity panel of 220 wild- and 25 cultivated-tomato varieties. We identified tolerant accessions with different RSA strategies; prioritizing lateral root elongation versus emergence. To identify genes involved in specific aspects of lateral root development, an F1 hybrid was generated that exhibited both parents combined characteristics. An F2-segregating population was then used to identify four distinct subpopulations for Bulk Segregant Analysis (BSA). Simultaneously, we conducted Genome-Wide-Association Studies (GWAS) on root architecture of wild-tomato accessions under salt stress. By integrating the results of BSA and GWAS, we identified 22 candidates involved in the maintenance of root architecture. We utilized RNA-Seq to examine transcriptome reprogramming of the 22 genes in tomato accessions with contrasting lateral root responses. This approach resulted in the identification of 2 genes, AP2-like-ethylene-responsive transcription factor TOE3 and L-ascorbate peroxidase. Using exogenous ethylene, we demonstrated that root architecture exhibits plasticity, which benefits the plant by reducing Na+ accumulation. We profiled H2O2 waves across root systems of tomatoes, emphasizing the role of ROS in maintaining root system architecture under salt stress. These findings provide novel genetic targets for enhancing salt resilience in tomatoes, opening avenues for future research and breeding programs.

plant biology↗

bioRxiv2024

Natural variation in salt-induced changes in root:shoot ratio reveals SR3G as a negative regulator of root suberization and salt resilience in Arabidopsis

Soil salinity is one of the major threats to agricultural productivity worldwide. Salt stress exposure alters root and shoot growth rates, thereby affecting overall plant performance. While past studies have extensively documented the effect of salt stress on root elongation and shoot development separately, here we take an innovative approach by examining the coordination of root and shoot growth under salt stress conditions. Utilizing a newly developed tool for quantifying the root:shoot ratio in agar-grown Arabidopsis seedlings, we found that salt stress results in a loss of coordination between root and shoot growth rates. We identify a specific gene cluster encoding domain-of-unknown-function 247 (DUF247), and characterize one of these genes as Salt Root:shoot Ratio Regulator Gene (SR3G). Further analysis elucidates the role of SR3G as a negative regulator of salt stress tolerance, revealing its function in regulating shoot growth, root suberization, and sodium accumulation. We further characterize that SR3G expression is modulated by WRKY75 transcription factor, known as a positive regulator of salt stress tolerance. Finally, we show that the salt stress sensitivity of wrky75 mutant is completely diminished when it is combined with sr3g mutation. Together, our results demonstrate that utilizing root:shoot ratio as an architectural feature leads to the discovery of new stress resilience gene. The studys innovative approach and findings not only contribute to our understanding of plant stress tolerance mechanisms but also open new avenues for genetic and agronomic strategies to enhance crop environmental resilience.

plant biology↗

bioRxiv2023

Deciphering Salt Stress Responses in Solanum pimpinellifolium through High-Throughput Phenotyping.

Soil salinity is a major environmental stressor affecting agricultural productivity worldwide. Understanding plant responses to salt stress is crucial for developing resilient crop varieties. Wild relatives of cultivated crops, such as wild tomato, Solanum pimpinellifolium, can serve as a useful resource to further expand the resilience potential of the cultivated germplasm, S. lycopersicum. In this study, we employed high-throughput phenotyping in the greenhouse and field conditions to explore salt stress responses of a S. pimpinellifolium diversity panel. Our study revealed extensive phenotypic variations in response to salt stress, with traits such as transpiration rate, shoot mass, and ion accumulation showing significant correlations with plant performance. We found that while transpiration was a key determinant of plant performance in the greenhouse, shoot mass strongly correlated with yield under field conditions. Conversely, ion accumulation was the least influential factor under greenhouse conditions. Through a Genome Wide Association Study, we identified candidate genes not previously associated with salt stress, highlighting the power of high-throughput phenotyping in uncovering novel aspects of plant stress responses. This study contributes to our understanding of salt stress tolerance in S. pimpinellifolium and lays the groundwork for further investigations into the genetic basis of these traits, ultimately informing breeding efforts for salinity tolerance in tomato and other crops.

plant biology↗

bioRxiv2023

Development of a mobile, high-throughput, and low-cost image-based plant growth phenotyping system

Nondestructive plant phenotyping is fundamental for unraveling molecular processes underlying plant development and response to the environment. While the emergence of high-through phenotyping facilities can further our understanding of plant development and stress responses, their high costs significantly hinder scientific progress. To democratize high-throughput plant phenotyping, we developed sets of low-cost image- and weight-based devices to monitor plant growth and evapotranspiration. We paired these devices with a suite of computational pipelines for integrated and straightforward data analysis. We validated the suitability of our system for large screens by evaluating a cowpea diversity panel for responses to drought stress. The observed natural variation was subsequently used for Genome-Wide Association Study, where we identified nine genetic loci that putatively contribute to cowpea drought resilience during early vegetative development. We validated the homologs of the identified candidate genes in Arabidopsis using available mutant lines. These results demonstrate the varied applicability of this low-cost phenotyping system. In the future, we foresee these setups facilitating identification of genetic components of growth, plant architecture, and stress tolerance across a wide variety of species.

plant biology↗

bioRxiv2022

Cell wall extensin arabinosylation is required for root directional response to salinity

Soil salinity is a major contributor to crop yield losses. To improve our understanding of root responses to salinity, we developed and exploit here a real-time salt-induced tilting assay (SITA). This method follows root growth upon both gravitropic and salt challenges, revealing that root bending upon tilting is modulated by salinity, but not by osmotic stress. Next, this salt-specific response was measured in 345 natural Arabidopsis accessions and we discovered a genetic locus, encoding for the cell-wall modifying enzyme EXTENSIN ARABINOSE DEFICIENT TRANSFERASE (ExAD), to be associated with root bending in salt. Extensins are a class of structural cell wall glycoproteins [hydroxyproline-rich glycoproteins (HRGPs)] which are post-translationally modified by O-glycosylation mostly in the form of hydroxyproline (Hyp)-arabinosylation. We show that salt induces ExAD-dependent Hyp-arabinosylation, influencing root bending responses and cell wall thickness. We report that roots of exad mutants, which lack extensin Hyp-Araf4 modifications, display increased root epidermal cell wall thickness and porosity and altered gravitropic root bending in salt, as well as a reduced salt avoidance response. Our results suggest that extensin modification via Hyp-arabinosylation represents a novel salt-specific cellular process that is required for the directional response of roots exposed to salinity.

plant biology↗

bioRxiv2021

A mathematical framework for analyzing wild tomato root architecture

The root architecture of wild tomato, Solanum pimpinellifolium, can be viewed as a network connecting the main root to various lateral roots. Several constraints have been proposed on the structure of such biological networks, including minimizing the total amount of wire necessary for constructing the root architecture (wiring cost), and minimizing the distances (and by extension, resource transport time) between the base of the main root and the lateral roots (conduction delay). For a given set of lateral root tip locations, these two objectives compete with each other -- optimizing one results in poorer performance on the other -- raising the question how well S. pimpinellifolium root architectures balance this network design trade-off in a distributed manner. Here, we describe how well S. pimpinellifolium roots resolve this trade-off using the theory of Pareto optimality. We describe a mathematical model for characterizing the network structure and design trade-offs governing the structure of S. pimpinellifolium root architecture. We demonstrate that S. pimpinellifolium arbors construct architectures that are more optimal than would be expected by chance. Finally, we use this framework to quantify structural differences between arbors grown in the presence of salt stress, classify arbors into four distinct architectural ideotypes, and test for heritability of variation in root architecture structure.

plant biology↗

bioRxiv2021

Towards increased shading potential: a combined phenotypic and genetic analysis of rice shoot architecture

Rice feeds more than half of the worlds human population. In modern rice farming, a major constraint for productivity is weed proliferation and the ecological impact of herbicide application. Increased weed competitiveness of commercial rice varieties requires enhanced shade casting to limit growth of shade-sensitive weeds and the need for herbicide. We aimed to identify traits that enhance rice shading capacity based on the canopy architecture and the underlying genetic components. We performed a phenotypic screen of a rice diversity panel comprised of 344 varieties, examining 13 canopy architecture traits linked with shading capacity in 4-week-old plants. The analysis revealed a vast range of phenotypic variation across the diversity panel. We used trait correlation and clustering to identify core traits that define shading capacity to be shoot area, number of leaves, culm and solidity (the compactness of the shoot). To simplify the complex canopy architecture, these traits were combined into a Shading Rank metric that is indicative of a plants ability to cast shade. Genome wide association study (GWAS) revealed genetic loci underlying canopy architecture traits, out of which five loci were substantially contributing to shading potential. Subsequent haplotype analysis further explored allelic variation and identified seven haplotypes associated with increased shading. Identification of traits contributing to shading capacity and underlying allelic variation presented in this study will serve future genomic assisted breeding programmes. The investigated diversity panel, including widely grown varieties, shows that there is big potential and genetic resources for improvement of elite breeding lines. Implementing increased shading in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture. One sentence summaryThrough screening a rice diversity panel for variation in shoot architecture, we identified traits corresponding to plant shading potential and their genetic constituents.

plant biology↗

bioRxiv2020

Genetic mapping of the early responses to salt stress in Arabidopsis thaliana

Salt stress decreases plant growth prior to significant ion accumulation in the shoot. However, the processes underlying this rapid reduction in growth are still unknown. To understand the changes in salt stress responses through time and at multiple physiological levels, examining different plant processes within a single setup is required. Recent advances in phenotyping has allowed the image-based estimation of plant growth, morphology, colour and photosynthetic activity. In this study, we examined the salt stress-induced responses of 191 Arabidopsis accessions from one hour to seven days after treatment using high-throughput phenotyping. Multivariate analyses and machine learning algorithms identified that quantum yield measured in the light-adapted state (Fv'/Fm') greatly affected growth maintenance in the early phase of salt stress, while maximum quantum yield (QY max) was crucial at a later stage. In addition, our genome-wide association study (GWAS) identified 770 loci that were specific to salt stress, in which two loci associated with QY max and Fv'/Fm' were selected for validation using T-DNA insertion lines. We characterised an unknown protein kinase found in the QY max locus, which reduced photosynthetic efficiency and growth maintenance under salt stress. Understanding the molecular context of the identified candidate genes will provide valuable insights into the early plant responses to salt stress. Furthermore, our work incorporates high-throughput phenotyping, multivariate analyses and GWAS, uncovering details of temporal stress responses, while identifying associations across different traits and time points, which likely constitute the genetic components of salinity tolerance.

plant biology↗

bioRxiv2019

The use of high throughput phenotyping for assessment of heat stress-induced changes in Arabidopsis

The worldwide rise in heatwave frequency poses a threat to plant survival and productivity. Determining the new marker phenotypes that show reproducible response to heat stress and contribute to heat stress tolerance is becoming a priority. In this study, we describe a protocol focusing on the daily changes in plant morphology and photosynthetic performance after exposure to heat stress using an automated non-invasive phenotyping system. Heat stress exposure resulted in an acute reduction of quantum yield of photosystem II and increased leaf angle. In the longer term, exposure to heat also affected plant growth and morphology. By tracking the recovery period of WT and mutants impaired in thermotolerance (hsp101), we observed that the difference in maximum quantum yield, quenching, rosette size, and morphology. By examining the correlation across the traits throughout time, we observed that early changes in photochemical quenching corresponded with the rosette size at later stages, which suggests the contribution of quenching to overall heat tolerance. We also determined that 6h of heat stress provides the most informative insight in plant responses to heat, as it shows a clear separation between treated and non-treated plants as well as WT and hsp101. Our work streamlines future discoveries by providing an experimental protocol, data analysis pipeline and new phenotypes that could be used as targets in thermotolerance screenings.

plant biology↗