Biology subjects

Bonter, I.

Publications and source records attributed to Bonter, I..

7 recordsLinked to original sources

bioRxiv2026

Functional diversification of ERF transcription factors in land plants

The ERF family is one of the largest families of plant-specific transcription factors, controlling diverse developmental processes and stress responses. Extensive gene duplication and redundancy in flowering plants have generated large ERF repertoires, complicating comparisons of ERF function across land-plant lineages. How ERF transcription factor repertoires and their functions have evolved across land plants remains poorly understood. Here, we reconstruct the phylogenetic relationships and expansion of ERF transcription factors across land plants and exploit the compact ERF repertoire of the model liverwort Marchantia polymorpha to investigate their functional diversification. Systematic gain-of-function analysis reveals that different clades of ERFs can drive distinct cell fate and reprogramming outcomes in Marchantia, in addition to stress-related functions. Interestingly, we found that MpERF2, the sole Group I ERF in Marchantia, phylogenetically related to the WIND clade, promotes rhizoid cell differentiation. This contrast with the role of the WIND clade in wound-induced regeneration in Arabidopsis. Heterologous expression of AtWIND1 in Marchantia was also capable of inducing rhizoid formation, supporting the hypothesis that this reprogramming capacity is conserved at the protein level. On the other hand, loss of MpERF2 reduced rhizoid coverage but did not significantly impair regeneration. These findings provide an evolutionary framework for understanding the functional evolution of ERF transcription factors and how conserved transcriptional regulators are co-opted into novel developmental programs during the radiation of land plants.

plant biology↗

bioRxiv2026

Marchantia stem cell maintenance and re-establishment are controlled by MpPIN1-mediated auxin transport and ARF signalling

Meristem organization in land plants depends on coordinated auxin distribution, transport and response, yet how these processes are integrated during vegetative growth of the gametophyte of non-seed plants remains poorly understood. Here, we describe dissection of the auxin network in the liverwort Marchantia polymorpha using a suite of endogenous and synthetic reporters. Quantitative imaging with the R2DII auxin response sensor revealed that the apical meristem is positioned at a stable auxin minimum, with auxin levels increasing toward differentiated tissues. This spatial configuration correlates with polar localization of the auxin efflux carrier MpPIN1 along the direction of auxin flux. Disruption of MpPIN1 alters auxin distribution and compromises tissue regeneration, but does not prevent initial meristem formation, indicating that PIN-mediated transport reinforces rather than defines stem-cell niche identity. Imaging of auxin response reporters and MpARF1 and MpARF2 knock-in reporters further revealed a constrained auxin response within the meristem, characterized by low auxin signalling, dependent on the inhibitory activity of MpARF2 in the stem cell zone. During regeneration, transient, oscillatory ARF dynamics were observed before stabilization of a new auxin minimum and re-establishment of normal meristem architecture. Together, our results are consistent with auxin responses in the Marchantia meristem being shaped by an incoherent feed-forward network topology that couples auxin flux, transcriptional constraint and niche permissiveness. This architecture provides a robust framework for stem-cell maintenance and re-establishment, revealing ancestral principles of meristem regulation in land plants. SUMMARY STATEMENTBy mapping hormone distribution at cellular resolution in the liverwort Marchantia polymorpha, we reveal fundamental principles governing how plants maintain and rebuild their stem cell niches.

Plant Biology↗

bioRxiv2026

Initiation of asexual reproduction by the AP2/ERF gene GEMMIFER in Marchantia polymorpha

Plants can propagate their own clones through asexual reproduction. Genetic and hormonal factors regulating asexual reproduction have begun to be elucidated in the liverwort Marchantia polymorpha, which produce asexual propagules called gemmae within the gemma cups. Here, we report an AP2/ERF family gene, GEMMIFER (MpGMFR), as a key regulator of asexual reproduction in M. polymorpha. Suppression of MpGMFR function using genome editing and amiRNA results in the loss of gemma and gemma cup formation. In contrast, activation of MpGMFR function using a dexamethasone inducible system promotes gemma and/or gemma cup formation depending on the induction conditions. Notably, transient strong activation of MpGMFR induced gemma initial cells at the meristem, which develop into mature gemmae capable of reproducing as new individuals after detachment. These results show that MpGMFR is necessary and sufficient for the initiation of asexual reproduction at the meristem. MpGMFR expression was detected from the meristem through to the early stages of gemma development including the gemma cup floor cells. MpGMFR expression precedes the expression of GEMMA CUP-ASSOCIATED MYB1 (MpGCAM1) in early gemma development, supporting the notion that MpGMFR initiates asexual reproduction. We anticipate this finding to be a foundation to study the evolution of extra meristem formation in plant bodies that may have made a significant contribution to the prosperity of plants on land.

plant biology↗

bioRxiv2025

Arsenic-sensing domain controls ACR3 transporter trafficking and function in Marchantia polymorpha

Arsenic, a toxic and carcinogenic metalloid, is a pervasive environmental contaminant that threatens human health through contaminated water and food. The efflux of As(III) via ACR3 transporters is an ancient detoxification mechanism conserved across prokaryotes, fungi, and plants, with the notable exception of angiosperms. Despite their evolutionary significance, plant ACR3s remain largely uncharacterized. Here, we demonstrate that MpACR3, the ACR3 orthologue from the liverwort Marchantia polymorpha, functions as a metalloid/proton antiporter, conferring resistance to arsenicals and moderate tolerance to antimony. Additionally, we uncover an arsenic-sensing domain within MpACR3 that regulates its intracellular trafficking. Under normal conditions, MpACR3 sorting to the plasma membrane is delayed, resulting in its retention within Golgi bodies. However, As(III) binding to three cysteine residues in the N-terminal cytosolic domain induces a conformational change that facilitates MpACR3 trafficking to the plasma membrane. Furthermore, mutational analysis of a conserved arginine-based motif reveals that the N-terminal domain not only controls MpACR3 accumulation at the plasma membrane but also modulates its transport activity. Importantly, this arsenic-sensing domain is conserved among plant ACR3 transporters, suggesting a plant-specific adaptation to arsenic toxicity.

plant biology↗

bioRxiv2025

The minimal cell-cycle control system in Marchantia as a framework for understanding plant cell proliferation

The regulation of cell division is broadly conserved across eukaryotes, governed by cyclins and cyclin-dependent kinases (CDKs) to coordinate progression through the cell cycle. Plants have evolved a complex set of cell-cycle genes with unique features. The high number of cyclin-CDK pairs in flowering plants complicates functional studies due to redundancy and diversification. It is critical to study simple systems in other plant lineages to better understand the functional integration of the cell-cycle control machinery and its evolution across land plants. Through a comprehensive phylogenetic analysis, we show that non-seed plants possess a simple repertoire of cyclin and CDK proteins, suggesting that the observed complexity in seed plants is a derived trait. The liverwort Marchantia polymorpha possesses a streamlined set of core cell cycle genes with minimal redundancy during vegetative development. Using single-cell RNA-seq and fluorescent reporters, we found a precise, phase-specific expression pattern for cell cycle genes. We demonstrated in vivo that only three cyclins are active, one at a given phase, without redundancy. Functional analyses revealed that MpCYCD;1 promotes cell cycle re-entry and disrupts differentiation, while overexpression of MpCYCA or MpCYCB;1 arrests the cell cycle, consistent with their respective roles at G1, S, and G2/M progression. Our findings highlight the functional conservation of mechanisms for cell-cycle control across eukaryotes and provide insights into its ancestral state, revealing a minimal set of functional components required for multicellular development. This study advances our understanding of fundamental aspects of cell-cycle regulation and opens new possibilities for engineering plant growth.

plant biology↗

bioRxiv2025

The ABCG1 transporter is required for terpene biosynthesis in the lumen of Marchantia polymorpha oil bodies.

Marchantia polymorpha oil bodies (OBs) are specialised cell structures housing a diverse array of C15-terpenes, called sesquiterpenes. These compounds are known for their roles as herbivore repellents, yet the enzymes responsible for the biosynthesis of their precursors (C5 isoprenoid units) remain poorly characterized. Discrepancies remain between enzyme localizations suggested by computational predictions and those observed in earlier experimental studies, complicating our understanding of terpene biosynthesis. We investigated the localization of isoprenoid biosynthetic enzymes using translational and transcriptional reporters, coupled with confocal microscopy. Most enzymes localized as predicted (e.g., cytosol, chloroplast and the endoplasmic reticulum), and OB cells were identified as the primary sites of terpene biosynthesis. To explore OBs as potential storage sites for terpenes, we attempted to produce exogenous but easily identifiable compounds in Marchantia, such as the diterpene taxadiene and the triterpene {beta}-amyrin. Targeting to OB cells resulted in measurable amounts of these compounds, but their yields remained unaffected by the over-expression of key precursor genes, underscoring challenges in redirecting metabolic flux. To further investigate terpene accumulation in OBs, we focused on ABCG1, an ABC transporter previously reported to localize at the OB membrane. Overexpression of ABCG1 in OB cells, alongside an exogenous sesquiterpene synthase, only increased the levels of endogenous sesquiterpenes, while CRISPR-mediated disruption of ABCG1 resulted in a dramatic reduction in sesquiterpene accumulation. These findings establish ABCG1 as a critical factor for sesquiterpene retention within OBs and provide new insights into the mechanisms governing terpene metabolism and storage in Marchantia polymorpha.

plant biology↗

bioRxiv2023

Mapping the landscape of transcription factor promoter activity during vegetative development in Marchantia

Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterising the transcriptional activity of TF genes in space and time is a critical step towards understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot-apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only [~]450 TF genes, Marchantia polymorpha is an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally tested in planta reporter fusions for all the TF promoters in the collection and systematically analysed expression patterns in Marchantia gemmae. This allowed us to build a map of precise expression domains and identify a unique set of TFs expressed in the stem-cell zone, providing new insight into the dynamic regulation of the gametophytic meristem and its evolution. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that the promoter elements characterised here will be useful for cell-type specific expression, synthetic biology applications, and functional genomics.

plant biology↗