Biology subjects

Prochazkova Schrumpfova, P.

Publications and source records attributed to Prochazkova Schrumpfova, P..

6 recordsLinked to original sources

bioRxiv2026

PWO1 and TRB proteins coordinate chromatin regulation to prevent premature differentiation and ectopic lignin deposition in Arabidopsis

The Arabidopsis PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 (PWO1) and Telomere Repeat-Binding Proteins 1-3 (TRB1-3, TRBs) associate with distinct and shared protein complexes involved in epigenetic regulation, yet their cooperative roles in chromatin control and plant development remain largely unexplored. Here, we show that the interaction between PWO1 and TRBs is evolutionarily conserved. Both PWO1 and TRBs associate with plant telomeres, interact at these regions, and are co-enriched at subsets of interspersed telo-box motifs across regulatory regions genome-wide. TRBs facilitate PWO1 binding at shared genomic regions, including telo-box motifs. PWO1 and TRBs share a substantial number of genomic targets and preferentially bind chromatin regions associated with transcriptionally active states, whereas TRBs alone associate with repressive marks at thousands of loci. Genetic analyses show that the pwo1 trb1 trb3 triple mutant displays severe developmental defects, including main stem arrest and early maturation associated with aberrant lignin deposition in interfascicular tissues. In the triple mutant, key enzymes in the lignin biosynthesis pathway are upregulated, indicating that PWO1, TRB1, and TRB3 cooperatively regulate secondary cell wall formation. Together, our findings provide new insights into how PWO1 and TRBs cooperate to regulate chromatin states and orchestrate plant development, highlighting their central role in controlling gene expression programs. Significance statementThis study shows that PWO1 and TRB proteins co-occupy telomeres, including interspersed telo-box motifs, to regulate chromatin organization and plant development, particularly ectopic lignin deposition. Our findings reveal how these nuclear protein factors coordinate epigenetic states in Arabidopsis thaliana, providing a framework for understanding the control of developmental programs. O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/740627v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1a3d544org.highwire.dtl.DTLVardef@1067082org.highwire.dtl.DTLVardef@1c49163org.highwire.dtl.DTLVardef@252171_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract:C_FLOATNO Evolutionarily conserved PWO-TRB interactions and their shared roles in chromatin regulation and plant development. Created with BioRender.com. C_FIG

plant biology↗

bioRxiv2025

HSP90-mediated stress resilience in male gametophyte of Arabidopsis thaliana

Despite the accumulation of protective heat shock proteins (HSPs) during the male gametophyte development, pollen grains are highly sensitive to elevated temperatures. We performed transcriptomic analysis of five pollen developmental stages isolated from plants under normal and heat stress (H) conditions; uni-nuclear (UN), early bi-cellular (EB), bi-cellular (BC), tri-cellular (TC), and mature pollen (MPG). We show that the majority of genes that are up- or down-regulated under HS are specific for each stage, except BC stage that also exhibited the highest number of differentially expressed genes (DEGs) (>4000). This emphasize a complex, stage-dependent heat stress response, possibly dependent on HSP levels. Additionally, promoter motif analysis revealed that heat shock elements (HSEs) exhibit a stage- specific pattern of enrichment, which peaked in MP. To explore stage-specific influences of HSP90s in pollen development, we characterized a knockdown RNAi line, under normal and stress conditions in early- and late-stage RNAi lines using stage-specific promoters pJASON (JA90R) and pLAT52 (L90R). The hsp90 background leads to lower germination rate in both RNAi lines that is more pronounced under heat stress caused by significant alterations in heat stress control via impaired ABA signalling or ER stress response. Heat stress conditions also lead to a high percentage of nuclei shape and orientation defects in the L90R line pollen, pointing to the higher sensitivity of late stage development. We show this defect is linked to the down-regulation of DNA metabolism genes. Our complex dataset provides insight into stage-specific stress response on the level of single cell undergoing developmental changes.

plant biology↗

bioRxiv2025

Molecular and Phenotypic Characterization of Telomere Repeat Binding (TRBs) Proteins in Moss: Evolutionary and Functional Perspectives

Telomere repeat binding (TRB) proteins are plant-specific proteins with a unique domain structure distinct from telomere-binding proteins in animals and yeast. While extensively studied in seed plants, their role in early-diverging plant lineages remain largely unexplored. Here, we investigate TRB proteins in a model moss, Physcomitrium patens, to assess their evolutionary conservation and functional significance. Functional analysis using single knockout mutants revealed that individual PpTRB genes are essential for normal development, with mutants exhibiting defects in the two-dimensional (protonemal) stage and, more prominently, in the formation of three-dimensional (gametophore) structures. Some double mutants displayed telomere shortening, a phenotype also observed in TRB-deficient seed plants, indicating a conserved role for TRBs in telomere maintenance. Transcriptome profiling of TRB mutants revealed altered expression of genes associated with transcriptional regulation and stimulus response in protonema. Subcellular localization studies across various plant cell types confirmed that PpTRBs, like their seed plant counterparts, localize prevalently to the plant nucleus and mutually interact. In bryophytes, TRBs form a monophyletic group that mirrors the species phylogeny, whereas in seed plants, TRBs have diversified into two distinct monophyletic groups. Our findings provide the first comprehensive characterization of TRB proteins in non-vascular plants and demonstrate their conserved roles in telomere maintenance, with additional implications for plant development and gene regulation across land plant lineages. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/659030v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1fea36dorg.highwire.dtl.DTLVardef@9b5569org.highwire.dtl.DTLVardef@488d0org.highwire.dtl.DTLVardef@1b22c6b_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2024

GOLEM: A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte

BackgroundThe regulation of gene expression during tissue development is very complex. A key mechanism of gene regulation is the recognition of regulatory motifs, also known as cis-regulatory elements (CREs), by various proteins in gene promoter regions. Localization of these motifs near the transcription start site (TSS) or translation start site (ATG) is crucial for transcription initiation and rate. Transcription levels of individual genes, regulated by these motifs, can vary significantly across tissues and developmental stages, especially in processes like sexual reproduction. However, the precise localization and visualization of regulatory motifs in relation to gene expression in specific tissues can be challenging. ResultsHere, we introduce a program called GOLEM (Gene regulatOry eLEMents) which enables users to precisely locate any motif of interest with respect to TSS or ATG within the relevant plant genomes across the plant Tree of Life (Marchantia, Physcomitrium, Amborella, Oryza, Zea, Solanum and Arabidopsis). The visualization of the motifs is performed with respect to the transcript levels of particular genes in leaves and male reproductive tissues and can be compared with genome-wide distribution regardless of the transcription level. Additionally, genes with specific CREs at defined positions and high expression in selected tissues can be exported for further analysis. GOLEMs functionality is illustrated by its application to conserved motifs (e.g. TATA-box, ABRE, I-box, and TC-element), as well as to male gametophyte-related motifs (e.g. LAT52, MEF2, ARR10_core, and DOF_core). ConclusionGOLEM is a freely available tool (https://golem.ncbr.muni.cz) for tracking the precise localization and distribution of any CREs of interest in plant gene promoters. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=59 SRC="FIGDIR/small/606583v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@13c1fc9org.highwire.dtl.DTLVardef@4b034dorg.highwire.dtl.DTLVardef@c5e28aorg.highwire.dtl.DTLVardef@19c0ce4_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

Shoot phenotyping of cytokinin receptors mutants revealed fluorescence parameters as early markers of drought stress

Plant phenotyping represents an increasing promise in plant research by providing a complex picture of plant development and fitness. In research focused on various environmental stresses, phenotyping can uncover markers that can sensitively assess the stress impact in very early stages before morphological changes. PlantScreenTM System represents a tool dedicated for shoot and root phenotyping in soil enabling high-precision, high-throughput phenotyping of small, mid-size and large plants. The system offers wide range of sensors providing the number of non-invasive analyses of morphological and physiological parameters as well as of pigments, water, or metabolite content. In our work, we combined phenotyping approaches to determine morphological changes and the status of the photosynthetic apparatus in Arabidopsis plants exposed to drought stress. Focused on morphology, the rosette area became smaller after seven days of drought stress when compared to control conditions. Interestingly, cytokinin signalling mutant ahk2 ahk3 revealed drought resistance compared to other genotypes. The fluorescent parameters showed higher sensitivity even in wild type. Non-photochemical quenching displayed values connected to reduced activity of photosynthetic apparatus after five days of drought stress. Taken together, acquired fluorescence parameters can serve as a marker of drought stress detection before morphological alterations occur. HighlightFluorescence parameters can serve as early markers of drought stress before morphological alterations appear. Shoot phenotyping of cytokinin receptor mutants showed drought resistance in the ahk2 ahk3 double mutant.

plant biology↗

bioRxiv2020

Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis

While the pivotal role of linker histone H1 in shaping nucleosome organization is well established, its functional interplays with chromatin factors along the epigenome are just starting to emerge. Here we first report that in Arabidopsis, as in mammals, H1 occupies Polycomb Repressive Complex 2 (PRC2) target genes where it favors chromatin condensation and H3K27me3 deposition. We further show that, contrasting with its conserved function in PRC2 activation at genes, H1 selectively prevents H3K27me3 accumulation at telomeres and large pericentromeric interstitial telomeric repeat (ITR) domains by restricting DNA accessibility to Telomere Repeat Binding (TRB) proteins, a group of H1-related Myb factors mediating PRC2 cis recruitment. This study unveils a mechanistic framework by which H1 avoids the formation of gigantic H3K27me3-rich domains at telomeric sequences and contributes to safeguard nucleus architecture. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/402172v5_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@13cf29dorg.highwire.dtl.DTLVardef@5c5c86org.highwire.dtl.DTLVardef@1be7516org.highwire.dtl.DTLVardef@f935cb_HPS_FORMAT_FIGEXP M_FIG Teano et al. report that that linker histone H1 and a group of H1-related telomeric proteins interplay to selectively influence the Polycomb repressive landscape at genes and telomeric repeats in Arabidopsis. These findings provide a mechanistic framework by which H1 influences the epigenome and nuclear organization in a sequence-specific manner. C_FIG HighlightsO_LIH1 promotes PRC2 activity and limits accessibility at a majority of genes C_LIO_LIH1 prevents PRC2 activity at telomeric DNA sequences C_LIO_LIPRC2 repression is achieved by restricting accessibility to TRB proteins C_LIO_LIH1 orchestrates the spatial organization of telomeres and interstitial telomeres (ITRs) C_LI

molecular biology↗