Biology subjects

Adamkova, V.

Publications and source records attributed to Adamkova, V..

6 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

Engineering chromatin to encode transcriptional immune memory in Arabidopsis

Transcriptional memory enables organisms to respond more rapidly to recurrent stress, yet the underlying features of chromatin that contribute to this transcriptional recalibration remain poorly defined. Here we identify the genes displaying transcriptional memory in response to the bacterial immune elicitor, flg22, in Arabidopsis thaliana. In comparison to non-memory response genes, these memory genes show a preference for tissue-specific over uniform spatial expression patterning. The chromatin architecture of these genes in the resting state displays depletion of H3K4me3, elevation H3K27me3 and a subset are marked by H3K27me3-H3K4me3 bivalency. The H3K4me3 demethylase, JMJ14, is required for transcriptional memory, with JMJ14 occupancy enriched over memory gene loci. Upon priming, chromatin is reconfigured, with H3K4me3 levels increasing in a sustained manner at memory gene loci. To assess the function of this H3K4me3 accrual, we employ epigenome-engineering, observing that its targeted deposition at memory gene loci, including the WRKY29 locus, is sufficient to drive transcriptional memory and can endow plants with enhanced resistance to the bacterial pathogen, Pseudomonas syringae. Together, the findings demonstrate a causal role for H3K4me3 in transcriptional memory, under the regulation of JMJ14, and open the door for rational rewriting of chromatin to enhance organismal resilience.

plant biology↗

bioRxiv2025

CRISPR targeting of H3K4me3 activates gene expression and unlocks centromeric crossover recombination in Arabidopsis

H3K4me3 is a fundamental and highly conserved chromatin mark across eukaryotes, playing a central role in many genome-related processes, including transcription, maintenance of cell identity, DNA damage repair, and meiotic recombination. However, identifying the causal function of H3K4me3 in these diverse pathways remains a challenge, and we lack the tools to manipulate it for agricultural benefit. Here we use the CRISPR-based SunTag system to direct H3K4me3 methyltransferases in the model plant, Arabidopsis thaliana. Targeting of SunTag-SDG2 activates the expression of the endogenous reporter gene, FWA. We show that SunTag-SDG2 can be employed to increase pathogen resistance by targeting the H3K4me3-dependent disease resistance gene, SNC1. Meiotic crossover recombination rates impose a limit on the speed with which new traits can be transferred to elite crop varieties. We demonstrate that targeting of SunTag-SDG2 to low recombining centromeric regions can significantly stimulate proximal crossover formation. Finally, we reveal that the effect is not specific to SDG2 and is likely dependent on the H3K4me3 mark itself, as the orthogonal mammalian-derived H3K4me3 methyltransferase, PRDM9, produces a similar effect on gene expression with reduced off-target potential. Overall, our study supports an instructive role for H3K4me3 in transcription and meiotic recombination and opens the door to precise modulation of important agricultural traits.

plant biology↗

bioRxiv2024

A helper NLR targets organellar membranes to trigger immunity

Upon activation, plant NLR immune receptors are known to assemble into oligomeric resistosomes that insert into the plasma membrane, forming Ca2+-permeable channels and triggering immunity. Here, we show that the RPW8-like coiled-coil (CCR-) NLR NRG1 primarily targets organelles instead of the plasma membrane. Unlike canonical CC-NLRs, activated NRG1 accumulates at the chloroplast envelope and channels stromal Ca2+ into the cytosol. AlphaFold modeling of the NRG1 resistosome reveals an unusually long N-terminal membrane-insertion structure that would span the double chloroplast membranes. Nanobody-mediated relocalization shows functional membrane specificity: chloroplast trapping abolishes activity of the canonical helper CC-NLR NRC4 but not NRG1. NRG1 orthologs, from non-flowering lineages to angiosperms, target chloroplasts, suggesting that organelle-centered defense dates back to at least [~]360 million years. We propose that coiled-coil NLR diversification has enabled compartment-specific immune signaling to capture diverse Ca2+ stores.

plant biology↗

bioRxiv2024

The H3K4me3 binding ALFIN-LIKE proteins recruit SWR1 for gene-body deposition of H2A.Z

The H2A.Z histone variant is highly enriched over gene bodies, playing an essential role in several genome-templated processes, including transcriptional regulation and epigenetic patterning across eukaryotes. The SWR1 chromatin remodeling complex deposits H2A.Z. How SWR1 is directed to gene bodies is largely unknown. Here, we show that ALFIN-LIKE (AL) proteins are responsible for H2A.Z gene body patterning in Arabidopsis. AL proteins encode H3K4me3-binding PHD domains, and by ChIP-seq, we confirm preferential binding of AL5 to H3K4me3 over H3K4me1/2 in planta. We observe a global reduction in H2A.Z in al septuple mutants (al7m), especially of over H3K4me3-enriched genic regions. While MBD9 recruits SWR1 to nucleosome-free regions, ALs act non-redundantly with MBD9 for deposition of H2A.Z. Notably, al7m mutants show severe developmental abnormalities and upregulation of H2A.Z gene body-enriched responsive genes. Therefore, we propose a model whereby AL proteins direct gene body enrichment of H2A.Z by recruiting SWR1 to H3K4me3-containing responsive genes.

plant biology↗

bioRxiv2020

Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein

The development of a vaccine against COVID-19 is a hot topic for many research laboratories all over the world. Our aim was to design a semi-split inactivated vaccine offering a wide range of multi-epitope determinants important for the immune system including not only the spike (S) protein but also the envelope, membrane and nucleocapsid proteins. We designed a semi-split vaccine prototype consisting of S protein-depleted viral particles and free S protein. Next, we investigated its immunogenic potential in BALB/c mice. The animals were immunized intradermally or intramuscularly with the dose adjusted with buffer or addition of aluminum hydroxide, respectively. The antibody response was evaluated by plasma analysis at 7 days after the first or second dose. The immune cell response was studied by flow cytometry analysis of splenocytes. The data showed a very early onset of both S protein-specific antibodies and virus-neutralizing antibodies at 90% inhibition regardless of the route of vaccine administration. However, significantly higher levels of neutralizing antibodies were detected in the intradermally (geometric mean titer - GMT of 7.8 {+/-} 1.4) than in the intramuscularly immunized mice (GMT of 6.2 {+/-} 1.5). In accordance with this, stimulation of cellular immunity by the semi-split vaccine was suggested by elevated levels of B and T lymphocyte subpopulations in the murine spleens. These responses were more predominant in the intradermally immunized mice compared with the intramuscular route of administration. The upward trend in the levels of plasmablasts, memory B cells, Th1 and Th2 lymphocytes, including follicular helper T cells, was confirmed even in mice receiving the vaccine intradermally at a dose of 0.5 g. We demonstrated that the semi-split vaccine is capable of eliciting both humoral and cellular immunity early after vaccination. Our prototype thus represents a promising step toward the development of an efficient anti-COVID-19 vaccine for human use.

microbiology↗