Biology subjects

Lee, R. R. Q.

Publications and source records attributed to Lee, R. R. Q..

4 recordsLinked to original sources

bioRxiv2025

Transcriptome Reprogramming Associated with Autoimmunity Reveals Key Points of the Growth-Defence Trade-off in Arabidopsis thaliana

Growth and defence are inversely correlated processes requiring balance for optimal fitness. While each is well studied, their regulatory trade-offs are less understood. Using DANGEROUS MIX (DM) autoimmune plants with stunted growth in Arabidopsis thaliana, we investigated the balancing act. Transcriptome analysis of three DM cases and pathogen-treated seedlings identified two major modules representing defence and growth. These core modules, comprising 4,712 genes ([~]17% of the transcriptome), were sufficient for projecting the trade-off across immune transcriptome meta-datasets. Removing all three ADR1s, the helper NLRs, reversed the expression patterns of both modules and shifted the trade-off balance. ADR1s had a stronger impact on growth-associated RLK genes than on defence genes. Autoimmune plants also showed greater chromatin accessibility changes in growth loci than in defence loci. Our findings suggest an unexpected mechanism where immune signalling, partly mediated by ADR1s, actively suppresses growth genes, providing a strategy to regulate the growth-defence trade-off.

plant biology↗

bioRxiv2024

Structure determinants of DANGEROUS MIX 3, an alpha/beta hydrolase, for triggering NLR-mediated genetic incompatibility in plants

Genetic incompatibility occurs when a mismatched pair of plant immune components mounts autoimmune responses in hybrids. Highly diversified NLR receptors are main culprits of the genetic conflict, recognizing host proteins from different origin as immune trigger. Here, we report the molecular mechanism underlying a DANGEROUS MIX (DM) autoimmunity, comprising DM2h/RPP1 NLR and its incompatible partner DM3, an alpha/beta hydrolase. Cryo-electron microscopy reveals the oligomeric nature of two natural DM3 variants in a trimer of dimer configuration. The polymorphism triggering autoimmunity is located at the dimer interface, resulting in drastic structural differences such that dimerizing helix and loop reinforcing the interface is lost and disordered. Structure-function analysis shows that integrity of the dimer interface, but neither maintenance of hexamer nor its enzymatic activity, is the key factor contributing to autoimmunity. Our finding pinpoints checkpoints embedded in the oligomeric configuration of a host enzyme that controls the switching mechanism of NLR activity.

plant biology↗

bioRxiv2022

Generating minimum set of gRNA to cover multiple targets in multiple genomes with MINORg

MINORg is an offline gRNA design tool that generates the smallest possible combination of gRNA capable of covering all desired targets in multiple non-reference genomes. As interest in pangenomic research grows, so does the workload required for large screens in multiple individuals. MINORg aims to lessen this workload by capitalising on sequence homology to favour multi-target gRNA while simultaneously screening multiple genetic backgrounds in order to generate reusable gRNA panels. We demonstrated the practical application of MINORg by knocking out a 11 homologous genes tandemly arrayed in a multigene cluster in two Arabidopsis thaliana lineages using three gRNA output by MINORg. Source code is freely available at https://github.com/rlrq/MINORg.

bioinformatics↗

bioRxiv2020

A singleton NLR of recent origin causes hybrid necrosis in Arabidopsis thaliana

Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. We investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies three weeks after sowing. Massive transcriptional changes take place in the hybrid, including the upregulation of most NLR disease resistance genes. This is due to an incompatible interaction between the singleton TIR-NLR gene DANGEROUS MIX 10 (DM10), which was recently relocated from a larger NLR cluster, and an unlinked locus, DANGEROUS MIX 11 (DM11). There are multiple DM10 allelic variants in the global A. thaliana population, several of which have premature stop codons. One of these, which has a truncated LRR domain, corresponds to the DM10 risk allele. The DM10 locus and the adjacent genomic region in the risk allele carriers are highly differentiated from those in the non-risk carriers in the global A. thaliana population, suggesting that this allele became geographically widespread only relatively recently. The DM11 risk allele is much rarer and found only in two accessions from southwestern Spain - a region from which the DM10 risk haplotype is absent - indicating that the ranges of DM10 and DM11 risk alleles may be non-overlapping.

evolutionary biology↗