Biology subjects

Kunze, R.

Publications and source records attributed to Kunze, R..

3 recordsLinked to original sources

bioRxiv2024

Butterfly eggs prime anti-herbivore defense in an annual but not perennial Arabidopsis species

While plant anti-herbivore defenses of the annual plant species Arabidopsis thaliana were shown to be primable by Pieris brassicae eggs, the primability of the phylogenetically closely related perennial Arabidopsis lyrata has not yet been investigated. Previous studies revealed that closely related wild Brassicaceae plant species, the annual Brassica nigra and the perennial Brassica oleracea, exhibit an egg-primable defense trait, even though they have different life spans. Here, we tested whether P. brassicae eggs prime anti-herbivore defenses of the perennial A. lyrata. We exposed A. lyrata to P. brassicae eggs and larval feeding and assessed their primability by i) determining the biomass of P. brassicae larvae after feeding on plants with and without prior P. brassicae egg deposition and ii) investigating the plant transcriptomic response after egg deposition and/or larval feeding. For comparison, these studies were also conducted with A. thaliana. Consistent with previous findings, A. thalianas response to prior P. brassicae egg deposition negatively affected conspecific larvae feeding upon A. thaliana. However, this was not observed in A. lyrata. Arabidopsis thaliana responded to P. brassicae eggs with strong transcriptional reprogramming, whereas A. lyrata responses to eggs were negligible. In response to larval feeding, A. lyrata exhibited a greater transcriptome change compared to A. thaliana. Among the strongly feeding-induced A. lyrata genes were those that are egg-primed in feeding-induced A. thaliana, i.e., CAX3, PR1, PR5 and PDF1.4. These results suggest that A. lyrata compensates for its lack of egg-mediated primability by a stronger response to larval feeding.

plant biology↗

bioRxiv2023

SPPiDDRs: a new gene family in dicot plants involved in DNA-Damage Response

Living organisms must maintain the integrity of their genome, and plants are not exempt. In plants, recognition of DNA damage converges at the transcription factor SOG1, a functional homolog of the animal p53 protein. SOG1 directly controls the expression of hundreds of genes and orchestrates a sophisticated network of signaling pathways termed DNA-damage response (DDR). Only recently, several long non-coding RNA (lncRNA) loci were identified to be upregulated by DNA damage, and only a handful have been confirmed to actively contribute to DDR. In this study, we focused on one locus annotated as lncRNA and found that it is strongly and quickly upregulated upon DNA damage and is a direct target of SOG1. Combining in silico and experimental analyses, we demonstrate that this locus was wrongly annotated as lncRNA and is in fact a gene coding for a short protein that targets peroxisomes. Consequently, we renamed this locus SHORT PEROXISOMAL PROTEIN INDUCED IN DNA-DAMAGE RESPONSE1 (SPPiDDR1). SPPiDDRs are well conserved and present in multiple copies across dicot genomes, with Arabidopsis containing two additional copies, SPPiDDR2 and SPPiDDR3. The AtSPPiDDR paralogs differ on the transcriptional level, SPPiDDR3 being the least active. SPPiDDR1 and SPPiDDR2 are both also induced by salt, a stress treatment known to indirectly induce DNA damage via oxidative stress. We show that these two genes act redundantly and inhibit plant growth in response to salt stress.

molecular biology↗

bioRxiv2023

The long non-coding RNA LINDA restrains cellular collapse following DNA damage in Arabidopsis thaliana

The genomic integrity of every organism is endangered by various intrinsic and extrinsic stresses. To maintain the genomic integrity, a sophisticated DNA damage response (DDR) network is activated rapidly after DNA damage. Notably, the fundamental DDR mechanisms are conserved in eukaryotes. However, knowledge about many regulatory aspects of the plant DDR is still limited. Important, yet little understood, regulatory factors of the DDR are the long non-coding RNAs (lncRNAs). In humans, 13 lncRNAs functioning in DDR have been characterized to date, whereas no such lncRNAs have been characterized in plants yet. By meta-analysis, we identified the long intergenic non-coding RNA induced by DNA damage (LINDA) that responds strongly to various DNA double-strand break-inducing treatments, but not to replication stress induced by mitomycin C. After DNA damage, LINDA is rapidly induced in an ATM- and SOG1-dependent manner. Intriguingly, the transcriptional response of LINDA to DNA damage is similar to that of its flanking hypothetical protein-encoding gene. Phylogenetic analysis of putative Brassicales and Malvales LINDA homologs indicates that LINDA lncRNAs originate from duplication of a flanking small protein-encoding gene followed by pseudogenization. We demonstrate that LINDA is not only needed for the regulation of this flanking gene, but also for fine-tuning of the DDR after the occurrence of DNA double-strand breaks. Moreover, {Delta}linda mutant root stem cells are unable to recover from DNA damage, most likely due to hyper-induced cell death. SIGNIFICANT STATEMENTWe unraveled the functional relevance of the first lncRNA within the DNA damage response network of Arabidopsis thaliana. This lncRNA, termed LINDA, is an important part of the DNA damage response network, as it is needed for accurate regulation of cell death and cell cycle progression.

plant biology↗