Biology subjects

Stahl, Y.

Publications and source records attributed to Stahl, Y..

15 recordsLinked to original sources

bioRxiv2026

A single-cell transcriptome atlas of the barley root apical meristem uncovers conserved and divergent roles of HvWOX5

Single-cell approaches have transformed plant developmental biology; however, cell-type-resolved resources for cereals remain limited. Here, we present a single-cell transcriptome atlas of the barley root apical meristem (RAM), which resolves 24 transcriptionally distinct cell populations. We assigned major root cell identities by integrating marker gene validation using Hybridization Chain Reaction (HCR) RNA fluorescence in situ hybridization and spatial transcriptomics with cross-species comparisons of published root atlases. Pseudotime analysis reconstructed developmental trajectories from the quiescent center to differentiating tissues, supporting the spatial and developmental organization of the atlas. We further demonstrated the utility of this resource by identifying HvWOX5 expression in the quiescent center and metaxylem and showing that HvWOX5 loss-of-function mutants displayed reduced root and meristem lengths, altered stem cell niche homeostasis, and disrupted metaxylem organization. Taken together, this atlas provides a framework for dissecting barley root development and identifies HvWOX5 as a key regulator of RAM organization and metaxylem patterning.

Plant Biology↗

bioRxiv2026

The Bacterial Kinase AnmK Integrates into Tick Genome and Biology

Horizontal Gene Transfer (HGT) contributes to eukaryotic evolution, potentially bringing phenotypic novelties to the recipient organisms. Ticks pose a severe threat to human health as vectors of various pathogens, including viruses, bacteria and protozoa, while stably hosting endosymbiotic bacteria. As such, these obligate blood-feeding parasites have been and continue to be exposed to HGT from a broad range of donors. To determine whether bacterial-to-tick HGT has contributed to important tick traits, we surveyed Ixodes tick genomes for HGT events. We revealed duplications of the known bacteria-derived gene dae2 and discovered two novel cases of bacterial HGT, the most remarkable of which involves a bacterial peptidoglycan metabolic gene (anmK) acquired by the common ancestor of ticks. The acquisition of an intron demonstrates "eukaryotization" of anmK within tick genomes. Transcript profiling revealed that anmK expression is upregulated during blood feeding, peaking in female ovaries, a niche occupied by horizontally acquired endosymbionts. Biochemical analysis confirmed that, to some extent, recombinant AnmK retains kinase activity on its cognate substrate - the bacterial cell wall component 1,6-anhydro-N-acetylmuramic acid. Immunolocalization showed that the enzyme is predominantly localized towards outer layers of the vitellogenic oocytes. Silencing of anmK in different tick species compromised blood-feeding and reproduction, demonstrating that this domesticated bacterial enzyme underpins reproductive fitness across tick species. Our findings exemplify the ability of horizontally acquired genes to integrate into the host biology and thereby shape host life history.

evolutionary biology↗

bioRxiv2026

EARLY FLOWERING 3 (ELF3): a novel role in integrating environmental stimuli with root stem cell niche maintenance

Maintaining stem cell niche (SCN) homeostasis in the root apical meristem (RAM) is essential for proper root growth and thus for overall plant development. In Arabidopsis thaliana, a group of slowly dividing cells at the SCN center known as the quiescent center (QC) maintain the surrounding stem cells, including the distally located columella stem cells (CSCs) which give rise to the differentiated columella cells. Many actors, including the PLETHORA (PLT) family transcription factors, regulate the QC quiescence and CSC fate. However, little is known about the integration of external and/or internal cues into regulating SCN homeostasis. In this study, we report for the first time the interaction between PLT3 and the thermosensor and circadian clock related transcriptional regulator, EARLY FLOWERING 3 (ELF3), which are both expressed in the root SCN. We show that ELF3 localizes, similar to PLT3, to subcellular condensates and sustains the QC and CSC fate. We demonstrate that ELF3 forms condensates in vitro and in vivo, in the cytoplasm, as well as in the nucleus, where it then co-localizes with PLT3. We reveal that the interaction of ELF3 and PLT3 is mediated by their intrinsically disordered prion-like domains (PrDs). Furthermore, transient expression in human epithelial cells (HEp-2) cells and in Nicotiana benthamiana shows that PHYTOCHROME INTERACTING FACTORS 3 and 4 (PIF3/4) function as nuclear shuttles for ELF3, recruiting it to nuclear condensates, where it co-localizes with PLT3, PIF3, and PIF4. Accordingly, we propose a model where the co-localization and interactions of ELF3, PLT3, PIF3, and PIF4 represent a dynamic mechanism to integrate environmental signals into SCN maintenance and cell fate decisions.

plant biology↗

bioRxiv2025

Integration of auxin and cytokinin signalling in Arabidopsis root meristem maintenance through the secreted peptide CLE40

Plant meristems perpetually generate new cells for the initiation, growth and differentiation of various cell types and organs. CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) genes encode plant specific peptides exerting indispensable functions in a multitude of these developmental processes. Previously, we have described a CLE40 signaling module that regulates stemness in the distal root meristem (DRM). Here, we show that CLE40 is additionally needed to maintain the proximal root meristem (PRM). We demonstrate that in cle40 mutants, meristematic cells differentiate prematurely, resulting in shortened PRMs and ultimately, reduced root growth. Furthermore, we link these effects to increased cytokinin signaling that can be circumvented by preventing the perception of cytokinin. We highlight how increased cytokinin signaling leads to a change in auxin distribution mediated by SHORT HYPOCOTYL 2 (SHY2), which is ectopically activated if CLE40 is not active. Finally, we propose that the receptor BARELY ANY MERISTEM 1 (BAM1), but not its homolog BAM2, perceives CLE40 in the PRM.

developmental biology↗

bioRxiv2025

The bivalent epigenetic regulator ULTRAPETALA1 promotes the Arabidopsis floral transition via recruitment of Polycomb histone methyltransferases for H3K27me3 deposition at the FLC locus

Floral induction is a major transition during the plant life cycle that contributes to reproductive fitness in annual and perennial plants. Flowering occurs in response to multiple environmental and endogenous cues. In Arabidopsis thaliana, many of these cues converge on the regulation of the FLOWERING LOCUS C (FLC) gene, which encodes a MADS domain transcription factor that functions as the main floral repressor. Here we demonstrate that the bivalent epigenetic regulator ULTRAPETALA1 (ULT1) is both necessary and sufficient to promote flowering. We identify ULT1 as a novel component of the autonomous pathway (AP) and show that it accelerates flowering by directly repressing FLC transcription. We demonstrate that ULT1 physically associates with the SWINGER (SWN) and CURLY LEAF (CLF) histone methyltransferase components of Polycomb Repressive Complex 2 (PRC2) to regulate FLC transcription by altering the accumulation of H3K27me3 marks. Our data indicate that ULT1 promotes the floral transition by interacting with SWN and CLF to recruit PRC2 to the FLC locus to deposit repressive histone methylation and reduce transcription of this key floral repressor.

plant biology↗

bioRxiv2025

The Arabidopsis dehydrin ERD14 chaperones the BRL3 receptor to confer drought resistance

Brassinosteroid plant hormones are involved in growth, biotic and abiotic-stress signaling, but functional analysis of its multiple receptors has largely focused on the ubiquitously expressed BRASSINOSTEROID INSENSITIVE 1 (BR1). The vascular-expressed brassinosteroid receptor kinase BRI1-LIKE 3 (BRL3) has a specific and essential role in Arabidopsis adaptation to drought and elevated temperature. However, the mechanistic understanding of BRL3 function and regulation is scant. Here, we show the dehydrin ERD14 colocalizes with BRI1 and BRL3 at the plasma membrane and physically interacts with these receptors through the ERD14Lys domain for proper receptor recruitment. erd14 mutants internalize BRL3-GFP and revert drought-resistant BRL3 over-expression phenotypes. BRL3 activation and downstream signaling events, including dephosphorylation of BES1 transcription factor, depend on the chaperone function of ERD14. Our study shows how proper chaperoning by ERD14 regulates BRL3 subcellular localization and activity of the vascular receptor, prompting re-examination of models of brassinosteroid-receptor functional diversification in plant adaptation to abiotic stress from specific cells of the vascular systems.

plant biology↗

bioRxiv2024

Stem cell homeostasis in the root of Arabidopsis involves cell-type specific complex formation of key transcription factors

In Arabidopsis thaliana, the stem cell niche (SCN) within the root apical meristem (RAM) is maintained by an intricate regulatory network that ensures optimal growth and high developmental plasticity. Yet, many aspects of this regulatory network of stem cell quiescence and replenishment are still not fully understood. Here, we investigate the interplay of the key transcription factors (TFs) BRASSINOSTEROID AT VASCULAR AND ORGANIZING CENTRE (BRAVO), PLETHORA 3 (PLT3) and WUSCHEL-RELATED HOMEOBOX 5 (WOX5) involved in SCN maintenance. Phenotypical analysis of mutants involving these TFs uncover their combinatorial regulation of cell fates and divisions in the SCN. Moreover, interaction studies employing fluorescence resonance energy transfer fluorescence lifetime imaging microscopy (FRET-FLIM) in combination with novel analysis methods, allowed us to quantify protein-protein interaction (PPI) affinities as well as higher-order complex formation of these TFs. We integrated our experimental results into a computational model, suggesting that cell type specific profiles of protein complexes and characteristic complex formation, that is also dependent on prion-like domains in PLT3, contribute to the intricate regulation of the SCN. We propose that these unique protein complex signatures could serve as a read-out for cell specificity thereby adding another layer to the sophisticated regulatory network that balances stem cell maintenance and replenishment in the Arabidopsis root.

plant biology↗

bioRxiv2023

Phase separation and molecular ordering of the prion-like domain of the thermosensory protein EARLY FLOWERING 3

Liquid-liquid phase separation (LLPS) is an important mechanism enabling the dynamic compartmentalisation of macromolecules, including complex polymers such as proteins and nucleic acids, and occurs as a function of the physicochemical environment. In the model plant, Arabidopsis thaliana, LLPS by the protein EARLY FLOWERING3 (ELF3) occurs in a temperature sensitive manner and controls thermoresponsive growth. ELF3 contains a largely unstructured prion-like domain (PrLD) that acts as a driver of LLPS in vivo and in vitro. The PrLD contains a poly-glutamine (polyQ) tract, whose length varies across natural Arabidopsis accessions. Here, we use a combination of biochemical, biophysical and structural techniques to investigate the dilute and condensed phases of the ELF3 PrLD with varying polyQ lengths. We demonstrate that the dilute phase of the ELF3 PrLD forms a monodisperse higher order oligomer that does not depend on the presence of the polyQ sequence. This species undergoes LLPS in a pH and temperature-sensitive manner and the polyQ region of the protein tunes the initial stages of phase separation. The liquid phase rapidly undergoes aging and forms a hydrogel as shown by fluorescence and atomic force microscopies. Furthermore, we demonstrate that the hydrogel assumes a semi-ordered structure as determined by small angle X-ray scattering, electron microscopy and X-ray diffraction. These experiments demonstrate a rich structural landscape for a PrLD protein and provide a framework to describe the structural and biophysical properties of biomolecular condensates.

biophysics↗

bioRxiv2022

FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) accumulates in homo- and heterodimeric complexes in dynamic and inducible nuclear condensates associated with speckle components

Some nuclear proteins undergo condensation, but the functional importance remains often unclear. The basic helix-loop-helix (bHLH) FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) integrates internal and external signals to control iron acquisition and growth. The previously described C-terminal residues Ser271/272 allow FIT to form active complexes with subgroup Ib bHLH factors such as bHLH039. FIT has lower nuclear mobility than mutant FITmSS271AA. Here, we show that FIT undergoes a light-inducible subnuclear partitioning into nuclear condensates that we termed FIT nuclear bodies (NBs). FIT NB characteristics were examined using a standardized FIT NB analysis procedure coupled with different types of quantitative and qualitative microscopy-based approaches. FIT condensates were reversible and likely formed by liquid-liquid phase separation. FIT accumulated preferentially in FIT NBs versus nucleoplasm when engaged in protein complexes with itself and with bHLH039. FITmSS271AA, instead, localized to NBs with different dynamics. FIT colocalized with splicing and light signaling NB markers. The NB-inducing light conditions were linked with active FIT and elevated FIT target gene expression in roots. Hence, we conclude that inducible, highly dynamic FIT condensates form preferentially when transcription factor complexes are active. Inducible FIT nuclear condensates may affect nuclear mobility and integrate environmental and Fe nutrition signals. HighlightsO_LIFIT undergoes light-induced, reversible condensation and localizes to nuclear bodies (NBs), likely via liquid-liquid phase separation C_LIO_LIFunctionally relevant Ser271/272 defines an intrinsically disordered region and influences NB formation dynamics C_LIO_LINBs are preferential sites for FIT dimerization with FIT and bHLH039, dependent on Ser271/272 C_LIO_LIFIT NBs colocalize with NB markers related to splicing and light signaling C_LIO_LILight conditions inducing NBs are linked with active FIT, in agreement with elevated FIT target gene expression in roots C_LI

plant biology↗

bioRxiv2022

The Arabidopsis SHORTROOT network coordinates shoot apical meristem development with auxin dependent lateral organ initiation

Unlike animals, plants have the capacity to produce new organs post-embryonically throughout their entire life cycle. This is due to stem cells present in the shoot and the root apical meristems (SAM and RAM, respectively). In the SAM, stem cells are located in the central zone (CZ) where they divide slowly. Stem cell daughters are displaced laterally and enter the peripheral zone (PZ). Here, their mitotic activity increases, and lateral organ primordia (LOP) are formed. How the spatial arrangement of these different domains is initiated and controlled during SAM growth and development, and how sites of LOP are determined in the PZ is not yet completely understood. In the RAM, the GRAS family transcription factor SHORTROOT (SHR) acts as a master regulator of signalling pathways that maintain the root stem cell niche and control formation of ground tissue layers. We hypothesized that SHR could perform a similar role in the SAM, and found that SHR, together with its target transcription factors SCARECROW (SCR), SCARECROW-LIKE23 (SCL23) and JACKDAW (JKD), controls shoot meristem size by regulating cell division rates, and promotes formation of lateral organs. SHR, SCR, SCL23 and JKD are expressed in very distinct patterns in the SAM. Where these expression domains overlap, they can physically interact to activate expression of the key cell cycle regulator CYCLIND6;1 (CYCD6;1) and thereby promote the formation of new cell layers. In the PZ, upregulation of SHR expression at sites of organ initiation depends on the phytohormone auxin, acting through the auxin response factor MONOPTEROS (MP) and auxin response elements in the SHR promoter. In the CZ, the SHR-target SCL23 physically interacts with WUS, a key regulator of stem cell maintenance, and both SCL23 and WUS expression are subject to negative feedback regulation from stem cells through the CLAVATA signalling pathway. Together, our findings illustrate how SHR-dependent transcription factor complexes act in different domains of the shoot meristem to mediate cell division and auxin dependent organ initiation in the PZ, and coordinate this activity with stem cell maintenance in the CZ of the SAM.

plant biology↗

bioRxiv2021

Control of Arabidopsis shoot stem cell homeostasis by two antagonistic CLE peptide signalling pathways

Stem cell homeostasis in plant shoot meristems requires tight coordiantion between stem cell proliferation and cell differentiation. In Arabidopsis, stem cells express the secreted dodecapeptide CLAVATA3 (CLV3), which signals through the leucine-rich repeat (LRR)-receptor kinase CLAVATA1 (CLV1) and related CLV1-family members to downregulate expression of the homeodomain transcription factor WUSCHEL (WUS). WUS protein moves from cells below the stem cell domain to the meristem tip and promotes stem cell identity, together with CLV3 expression, generating a negative feedback loop. How stem cell activity in the meristem centre is coordinated with organ initiation and cell differentiation at the periphery is unknown. We show here that the CLE40 gene, encoding a secreted peptide closely related to CLV3, is expressed in the SAM in differentiating cells in a pattern complementary to that of CLV3. CLE40 promotes WUS expression via BAM1, a CLV1-family receptor, and CLE40 expression is in turn repressed in a WUS-dependent manner. Together, CLE40-BAM1-WUS establish a second negative feedback loop. We propose that stem cell homeostasis is achieved through two intertwined pathways that adjust WUS activity and incorporate information on the size of the stem cell domain, via CLV3-CLV1, and on cell differentiation via CLE40-BAM1.

plant biology↗

bioRxiv2020

The conserved plant PM19 protein functions as an osmosensor and regulator of germination

How plants perceive water, especially during the critical stages of seed formation and germination, is key to their survival. During development and germination, seeds undergo large changes in water content, down to around 10% during maturation and up to 90% again within 24 hours of germination. We find the evolutionary conserved Arabidopsis plasma membrane protein PM19L1 to be an osmosensor, regulating dormancy and germination under osmotic stress. The PM19L1 protein structurally resembles the yeast osmosensor Sho1, with four transmembrane domains, and PM19L1 complements the osmosensitive sho1 mutant. Arabidopsis pm19l1 mutants have enhanced dormancy and reduced germination under salt and osmotic stress, and enhanced ABA levels. In a striking parallel to osmosensing in yeast, signalling downstream of PM19L1 involves a MAP kinase signal transduction pathway. PM19L1 is a positive regulator of ABI3, which promotes the late maturation of the seed, and negatively regulates the ABI4 and ABI5 dormancy- regulating transcription factors. These results have implications for the study of dormancy, drought, and salinity tolerance in crops, and may provide an insight into evolutionary adaptation of plants to a terrestrial environment.

plant biology↗

bioRxiv2020

Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots

Root growth and development are essential features for plant survival and the preservation of terrestrial ecosystems. In the Arabidopsis primary root apex, stem-cell specific transcription factors BRAVO and WOX5 co-localize at the Quiescent Center (QC) cells, where they repress cell division so that these cells can act as a reservoir to replenish surrounding stem cells, yet their molecular connection remains unknown. Here, by using empirical evidence and mathematical modeling, we establish the precise regulatory and molecular interactions between BRAVO and WOX5. We found that BRAVO and WOX5 regulate each other besides forming a transcription factor complex in the QC necessary to preserve overall root growth and architecture. Our results unveil the importance of transcriptional regulatory circuits at the quiescent and stem cells to the control of organ initiation and growth of plant tissues.

plant biology↗

bioRxiv2019

PLETHORA and WOX5 interaction and subnuclear localisation regulates Arabidopsis root stem cell maintenance

Maintenance and homeostasis of the stem cell niche (SCN) in the Arabidopsis root is essential for growth and development of all root cell types. The SCN is organized around a quiescent center (QC) maintaining the stemness of cells in direct contact. The key transcription factors (TFs) WUSCHEL-RELATED HOMEOBOX 5 (WOX5) and PLETHORAs (PLTs) are expressed in the SCN where they maintain the QC and regulate distal columella stem cell (CSC) fate. Here, we describe the concerted mutual regulation of the key TFs WOX5 and PLTs on a transcriptional and protein interaction level. Additionally, by applying a novel SCN staining method, we demonstrate that both WOX5 and PLTs regulate root SCN homeostasis as they control QC quiescence and CSC fate interdependently. Moreover, we uncover that some PLTs, especially PLT3, contain intrinsically disordered prion-like domains (PrDs) that are necessary for complex formation with WOX5 and its recruitment to subnuclear microdomains/nuclear bodies (NBs) in the CSCs. We propose that this partitioning of PLT-WOX5 complexes to NBs, possibly by phase separation, is important for CSC fate determination.

plant biology↗

bioRxiv2017

Fluorescent reporter lines for auxin and cytokinin signalling in barley (Hordeum vulgare)

The phytohormones auxin and cytokinin influence the development and maintenance of plant stem cell niches. Although barley (Hordeum vulgare) is the fourth most abundant cereal crop plant, the knowledge about these important phytohormones in regard to the root and shoot stem cell niche in barley is still negligible. In this study, we analyse the influence of auxin and cytokinin on the barley root meristem and present reporter lines to describe the auxin and cytokinin signalling output. Application of high concentrations of auxin and cytokinin to barley seedlings had a negative influence on barley root and meristem growth. The expression of the cytokinin reporter TCSn revealed that cytokinin signalling mostly takes place in the stele cells proximal to the QC and in the differentiated root cap cells, but can additionally be activated in the root stem cell niche by cytokinin application. Analysing signalling targets of auxin showed that a homologue of AtPLT1, HvPLT1, is expressed in a similar way as AtPLT1 in Arabidopsis, in particular in the QC and the surrounding cells. Furthermore, a homologue of the auxin PIN transporters PIN1, HvPIN1, was expressed in the root and the shoot meristem and polarly localizes to the plasma membrane. Its expression is regulated by cytokinin and the intracellular localisation is affected by BFA. With this study, we provide a valuable tool set of fluorescent barley reporter lines for auxin and cytokinin.

plant biology↗