Biology subjects

Vanhercke, T.

Publications and source records attributed to Vanhercke, T..

5 recordsLinked to original sources

bioRxiv2026

EffectorGeneP: accurate gene annotation in pathogen genomes from infection transcriptomes

Accurate gene annotation is crucial for inference of biological knowledge from genomes. However, non-canonical genes such as orphan or single-exon genes as well as those residing in rapidly evolving regions are routinely dismissed in annotation pipelines. In filamentous pathogen genomes, this disproportionately affects the annotation of genes encoding disease-promoting effector proteins. We introduce EffectorGeneP, a machine learning tool that self-trains on transcript data, predicts the most likely coding sequence from transcripts and effectively separates bona fide genes from transcriptional noise. EffectorGeneP annotates over 95% of known effectors correctly, while other state-of-the-art methods annotate 15%-78%. We show that EffectorGeneP expands the predicted secretome of pathogens by over 50% and that high-throughput screening of an effector library in plant protoplasts uncovers the previously poorly annotated AvrSr26 gene family in the wheat stem rust fungus. EffectorGeneP decodes genomes at unprecedented resolution and will enable the study of biological processes in important pathogen species.

microbiology↗

bioRxiv2024

A wheat tandem kinase sensor activates an NLR helper to trigger immunity

Most plant resistance genes encode membrane-anchored receptor-like proteins or intracellular nucleotide-binding and leucine-rich repeat (NLR) receptors. In wheat and barley, tandem kinases (TKs) have emerged as a new class of resistance determinants. To understand the modus operandi of the wheat stem rust resistance protein Sr62TK, we identified two genetic interactors-- a host gene required for Sr62TK function and the corresponding fungal AvrSr62 effector. We discovered that the SR62 locus consists of a digenic module encoding Sr62TK and an NLR (Sr62NLR). AvrSr62 binds to the N-terminal kinase of Sr62TK. This triggers displacement of the C-terminal kinase allowing it to recruit Sr62NLR for activation of immune responses. Understanding the mechanism of this two-component resistance complex will help engineering and breeding for durable resistance.

plant biology↗

bioRxiv2023

Pooled effector library screening in protoplasts rapidly identifies novel Avr genes

Crop breeding for durable disease resistance is challenging due to the rapid evolution of pathogen virulence. While progress in resistance (R) gene cloning and stacking has accelerated in recent years 1-3, the identification of corresponding avirulence (Avr) genes in many pathogens is hampered by the lack of high-throughput screening options. To address this technology gap, we developed a platform for pooled library screening in plant protoplasts for rapid identification of interacting R/Avr pairs. We validated this platform by isolating known and novel Avr genes from wheat stem rust (Puccinia graminis f. sp. tritici) by screening a designed library of putative effectors against individual R genes. Rapid Avr gene identification provides molecular tools to understand and track pathogen virulence evolution by genotype surveillance and optimise R gene deployment and stacking strategies. This screening platform is broadly applicable to many crop pathogens, whilst also adaptable for screening genes involved in other protoplast-selectable traits.

plant biology↗

bioRxiv2020

Consensus mutagenesis and ancestral reconstruction provide insight into the substrate specificity and evolution of the front-end Δ6-desaturase family

Marine algae are a major source of omega ({omega})-3 long-chain polyunsaturated fatty acids ({omega}3-LCPUFAs), which are conditionally essential nutrients in humans and a target for industrial production. The biosynthesis of these molecules in marine algae begins with the desaturation of fatty acids by {Delta}6-desaturases and enzymes from different species display a range of specificities towards {omega}3 and {omega}6 LCPUFAs. In the absence of a molecular structure, the structural basis for the variable substrate specificity of {Delta}6-desaturases is poorly understood. Here we have conducted a consensus mutagenesis and ancestral protein reconstruction-based analysis of the {Delta}6-desaturase family, focusing on the {omega}3-specific {Delta}6-desaturase from Micromonas pusilla (Mp{Delta}6des) and the bispecific ({omega}3/{omega}6) {Delta}6-desaturase from Ostreococcus tauri (Ot{Delta}6des). Our characterization of consensus amino acid substitutions in Mp{Delta}6des revealed that residues in diverse regions of the protein, such as the N-terminal cytochrome b5 domain, can make important contributions to determining substrate specificity. Ancestral protein reconstruction also suggests that some extant {Delta}6-desaturases, such as Ot{Delta}6des, could have adapted to different environmental conditions by losing specificity for {omega}3-LCPUFAs. This dataset provides a map of regions within {Delta}6-desaturases that contribute to substrate specificity and could facilitate future attempts to engineer these proteins for use in biotechnology.

biochemistry↗

bioRxiv2019

A versatile high throughput screening platform for plant metabolic engineering highlights the major role of ABI3 in lipid metabolism regulation

Traditional functional genetic studies in crops are time-consuming, complicated and cannot be readily scaled up. The reason is that mutant or transformed crops need to be generated to study the effect of gene modifications on specific traits of interest. However, many crop species have a complex genome and a long generation time. As a result, it usually takes several months to over a year to obtain desired mutants or transgenic plants, which represents a significant bottleneck in the development of new crop varieties. To overcome this major issue, we are currently establishing a versatile plant genetic screening platform, amenable to high throughput screening in almost any crop species, with a unique workflow. This platform combines protoplast transformation and fluorescence-activated cell sorting. Here we show that tobacco protoplasts can accumulate high levels of lipids if transiently transformed with genes involved in lipid biosynthesis and can be sorted based on lipid content. Hence, protoplasts can be used as a predictive tool for plant lipid engineering. Using this newly established strategy, we demonstrate the major role of ABI3 in plant lipid accumulation. We anticipate that this workflow can be applied to numerous highly valuable metabolic traits other than storage lipid accumulation. This new strategy represents a significant step towards screening complex genetic libraries, in a single experiment and in a matter of days, as opposed to years by conventional means.

plant biology↗