Biology subjects

Heidstra, R.

Publications and source records attributed to Heidstra, R..

5 recordsLinked to original sources

bioRxiv2025

The Lettuce Expression Browser: from lab to LEB

Lettuce (Lactuca sativa L.) is an economically important leafy vegetable within the Asteraceae family, cultivated worldwide across diverse agricultural systems. Recent advances in genomic and transcriptomic resources have positioned lettuce as a promising model system for functional genomics in the Asteraceae. However, currently available gene expression datasets lack comprehensive tissue-specific resolution, primarily focus on a single cultivar and are not visualised in an interpretable manner, limiting their utility for broader genetic and physiological studies. To bridge this gap, we developed the Lettuce Expression Browser (LEB), a publicly available platform providing high-resolution gene expression maps across various organs, tissues and developmental stages in both cultivated and wild lettuce species. The LEB integrates transcriptomic data from finely dissected seedlings, shoot tissues at various developmental stages and seedlings subjected to abiotic stresses (salt and far-red), visualised using the ggPlantmap R package. This platform offers an intuitive interface for exploring gene expression patterns and serves as a valuable resource for those studying lettuce development, stress responses, and evolutionary genomics. The LEB is hosted on the LettuceKnow Web Portal (https://lettuce.bioinformatics.nl) and can be expanded to include additional datasets, enhancing its role as a key tool for lettuce research and crop improvement. Significance statementThe Lettuce Expression Browser (LEB) provides the first high-resolution gene expression atlas for both cultivated and wild lettuce species. This open-access resource enables detailed exploration of gene activity across development stages and stress conditions, advancing functional genomics in the Asteraceae family.

plant biology↗

bioRxiv2021

The dual role of the RETINOBLASTOMA-RELATED protein in the DNA damage response is spatio-temporally coordinated by the interaction with LXCXE-containing proteins.

Living organisms face threats to genome integrity caused by environmental challenges or metabolic errors in proliferating cells. To avoid the spread of mutations, cell division is temporarily arrested while repair mechanisms deal with DNA lesions. Afterwards, cells either resume division or respond to unsuccessful repair by withdrawing from the cell cycle and undergoing cell differentiation or cell death. How the success rate of DNA repair connects to the execution of cell death remains incompletely known, particularly in plants. Here we provide evidence that the Arabidopsis thaliana RETINOBLASTOMA-RELATED1 (RBR) protein, shown to play structural and transcriptional functions in the DNA damage response (DDR), coordinates these processes in time by successive interactions through its B-pocket sub-domain. Upon DNA damage induction, RBR forms nuclear foci; but the N849F substitution in the B-pocket, which specifically disrupts binding to LXCXE motif-containing proteins, abolishes RBR focus formation and leads to growth arrest. After RBR focus formation, the stress-responsive gene NAC044 arrests cell division. As RBR is released from nuclear foci, it can be bound by the conserved LXCXE motif in NAC044. RBR-mediated cell survival is inhibited by the interaction with NAC044. Disruption of NAC044-RBR interaction impairs the cell death response but is less important for NAC044 mediated growth arrest. Noteworthy, unlike many RBR interactors, NAC044 binds to RBR independent of RBR phosphorylation. Our findings indicate that the availability of the RBR B-pocket to interact with LXCXE-containing proteins couples RBR DNA repair functions and RBR transcriptional functions of in the cell death program.

plant biology↗

bioRxiv2021

Analysis of phloem trajectory links tissue maturation to cell specialization.

The mechanisms that allow cells in the plant meristem to coordinate tissue-wide maturation gradients with specialized cell networks are critical for indeterminate growth. Here, we reconstructed the protophloem developmental trajectory of 19 cells from cell birth to terminal differentiation at single cell resolution in the Arabidopsis root. We found that cellular specification is mediated near the stem cell niche by PHLOEM EARLY DOF (PEAR) transcription factors. However, the PEAR dependent differentiation program is repressed by a broad gradient of PLETHORA (PLT) transcription factors, which directly inhibit PEARs own direct target ALTERED PHLOEM DEVELOPMENT (APL). The dissipation of PLT gradient around 7 cells from the stem cell activates APL expression, and a subsequent transitional network that results in a "seesaw" pattern of mutual inhibition over developmental time. Together, we provide a mechanistic understanding of how morphogen-like maturation gradients interface with cell-type specific transcriptional regulators to stage cellular differentiation.

plant biology↗

bioRxiv2020

Knocking out SOBIR1 in Nicotiana benthamiana abolishes functionality of transgenic receptor-like protein Cf-4

The first layer of plant immunity is formed by pattern recognition receptors (PRRs) that are present at the cell surface and perceive extracellular immunogenic patterns. Receptor-like proteins (RLPs), such as the tomato (Solanum lycopersicum) PRR Cf-4 that provides resistance to the fungus Cladosporium fulvum secreting the matching avirulence factor Avr4, have an extracellular receptor domain consisting of leucine-rich repeats, but lack a cytoplasmic kinase domain for downstream signaling. RLPs constitutively interact with the receptor-like kinase SUPPRESSOR OF BIR1-1 (SOBIR1), thereby providing the receptor with a kinase domain, and recruit the co-receptor BRI-ASSOCIATED KINASE 1 (BAK1) upon their activation by a matching ligand. Trans-phosphorylation events, which can take place between the kinase domains of SOBIR1 and BAK1 after their association with the RLP, are thought to initiate downstream defense signaling. Currently, our knowledge on RLP/SOBIR1/BAK1-mediated defence initiation is limited and to understand the role of SOBIR1 in RLP function, we knocked out SOBIR1 and its close homolog SOBIR1-like in the model plant Nicotiana benthamiana, as well as in transgenic N. benthamiana stably expressing Cf-4. We observed that Cf-4 function is completely abolished in the knock-out mutants, and we show that these plants can be used to perform transient complementation studies with SOBIR1 mutants. Thereby, these mutants are an important tool to study the fundamentals of plant immunity mediated by RLPs.

plant biology↗

bioRxiv2017

Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia

Rhizobium nitrogen-fixing nodules are a well-known trait of legumes, but nodules also occur in other plant lineages either with rhizobium or the actinomycete Frankia as microsymbiont. The widely accepted hypothesis is that nodulation evolved independently multiple times, with only a few losses. However, insight in the evolutionary trajectory of nodulation is lacking. We conducted comparative studies using Parasponia (Cannabaceae), the only non-legume able to establish nitrogen fixing nodules with rhizobium. This revealed that Parasponia and legumes utilize a large set of orthologous symbiosis genes. Comparing genomes of Parasponia and its non-nodulating relative Trema did not reveal specific gene duplications that could explain a recent gain of nodulation in Parasponia. Rather, Trema and other non-nodulating species in the Order Rosales show evidence of pseudogenization or loss of key symbiosis genes. This demonstrates that these species have lost the potential to nodulate. This finding challenges a long-standing hypothesis on evolution of nitrogen-fixing symbioses, and has profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.

plant biology↗