Biology subjects

Jonckheere, V.

Publications and source records attributed to Jonckheere, V..

7 recordsLinked to original sources

bioRxiv2026

Systematic real-time profiling of Salmonella type III effector translocation provides quantitative resolution of the T3SS-1/T3SS-2 secretion dichotomy

Type III secretion systems (T3SSs) enable Salmonella to modulate host cell biology by delivering a diverse repertoire of effector proteins. Yet, the temporal dynamics of effector translocation during prolonged infection remain poorly defined. Here, we establish a systematic real-time framework for quantifying effector secretion and translocation by combining endogenous HiBiT-tagging with split NanoLuc-based detection. Using this approach, we monitored the translocation kinetics of all 39 currently annotated type III effectors (T3Es) in Salmonella enterica serovar Typhimurium SL1344 over a 24-hour infection of epithelial cells. This comprehensive analysis revealed temporally distinct translocation patterns, widespread mid- and late-stage effector delivery, and a quantitatively resolved functional overlap between T3SS-1 and T3SS-2-mediated secretion than previously appreciated. These findings provide a more refined view of effector deployment throughout infection and illuminate previously overlooked aspects of effector dynamics. Altogether, this work offers a detailed temporal map of effector dynamics during epithelial infection and establishes a scalable strategy for dissecting secretion system function across host-pathogen systems.

cell biology↗

bioRxiv2025

THE ROOT-KNOT NEMATODE EFFECTOR MJ-MSP18: A SWISS ARMY KNIFE FOR REPROGRAMMING PLANT IMMUNITY

Root-knot nematodes (Meloidogyne spp.) are obligatory plant root parasites whose effector proteins play a critical role in suppressing plant immunity. However, the effectors direct host targets and underlying molecular mechanisms remain poorly understood. Using TurboID-mediated proximity labeling in tomato (Solanum lycopersicum) hairy roots, we identified an interaction between the nematode effector Mj-MSP18 and the tomato BRASSINOSTEROID-SIGNALING KINASE 7 (Sl-BSK7). Yeast two-hybrid (Y2H) assays confirmed that this interaction is conserved in Arabidopsis thaliana and Nicotiana benthamiana. Additionally, yeast three-hybrid and luciferase complementation assays demonstrated that Mj-MSP18 disrupts the interaction between BSK7/8 and FLS2 in both yeast and in planta. Given that the BSK7/8-FLS2 interaction is essential for flg22-induced pattern-triggered immunity (PTI), this disruption likely accounts for the suppression of reactive oxygen species (ROS) production and callose deposition observed upon transient expression of Mj-MSP18 in flg22-treated N. benthamiana leaves. Correspondingly, Arabidopsis and tomato bsk7 mutants exhibited increased susceptibility to root-knot nematode infection. Furthermore, RNA-seq analysis of tomato hairy roots expressing Mj-MSP18 revealed extensive transcriptional reprogramming, including the downregulation of defence-related genes and hydrogen peroxide response pathways. In addition, Y2H screening identified Sl-MYB and Sl-MYC2 as additional interactors, linking Mj-MSP18 to phytohormone biosynthesis, particularly the brassinosteroid (BR) and salicylic acid (SA) pathways, as validated by targeted metabolite analysis. The conservation of Mj-MSP18 across Meloidogyne species suggests a broadly conserved mechanism for host immune suppression and phytohormone modulation.

plant biology↗

bioRxiv2025

Virotrap Reveals Salmonella SopB as A Ubiquitinated Cargo for Host ESCRT-0

The pathogenic bacterium Salmonella survives and replicates in host cells within a Salmonella-containing vacuole (SCV), a membranous niche it actively remodels via secreted effectors. The phosphoinositide phosphatase SopB is a key effector implicated in SCV biogenesis, yet its host protein interactome has remained incompletely defined. Using the mass spectrometry-based interactomics technology Virotrap, we identify a novel set of SopB-associated host proteins, including the ESCRT-0 subunit HGS and other membrane remodeling proteins. We demonstrate that SopB directly interacts with HGS via its ubiquitin-binding domains, and show that SopB promotes ESCRT-0 recruitment to the SCV, yet ultimately counteracts its anti-replicative effect. As the ESCRT machinery plays a central role in cargo sorting and membrane remodeling, we propose a new SopB-dependent strategy by which Salmonella hijacks host endosomal trafficking to build its intracellular niche.

microbiology↗

bioRxiv2023

Distinct dynamics and proximity networks of hub proteins at the prey-invading cell pole in a predatory bacterium

In bacteria, cell poles function as subcellular compartments where proteins localize during specific lifecycle stages, orchestrated by polar "hub" proteins. Whereas most described bacteria inherit an "old" pole from the mother cell and a "new" pole from cell division, polarizing cells at birth, non-binary division poses challenges for establishing cell polarity, particularly for daughter cells inheriting only new poles. We investigated polarity dynamics in the obligate predatory bacterium Bdellovibrio bacteriovorus, proliferating through filamentous growth followed by non-binary division within prey bacteria. Monitoring the subcellular localization of two proteins known as polar hubs in other species, RomR and DivIVA, revealed RomR as an early polarity marker in B. bacteriovorus. RomR already marks the future anterior poles of the progeny during the predators growth phase, in a define time window closely following the onset of divisome assembly and the end of chromosome segregation. In contrast to RomRs stable unipolar localization in the progeny, DivIVA exhibits a dynamic pole-to-pole localization. This behaviour changes shortly before division of the elongated predator cell, where DivIVA accumulates at all septa and both poles. In vivo protein interaction networks for DivIVA and RomR, mapped through endogenous miniTurbo-based proximity labeling, further underscore their distinct roles in cell polarization and the importance of the anterior "invasive" cell pole in prey-predator interactions. Our work emphasizes the strict spatiotemporal coordination of cellular processes underlying B. bacteriovorus proliferation, offering insights into the subcellular organization of bacteria with filamentous growth and non-binary division.

microbiology↗

bioRxiv2021

Big fish, little fish: N-terminal acetyltransferase Naa40p proteoforms caught in the act

NatD consist of the evolutionary conserved N-alpha acetyltransferase catalytic subunit Naa40p and is among the most selective N-terminal acetyltransferase (NAT) complexes identified to date. Here we identified a conserved 22 amino acid N-terminally truncated Naa40 proteoform named Naa40p25 or short Naa40 (Naa40S). Intriguingly, while upon ectopic expression in yeast, both Naa40p proteoforms were capable of restoring N-terminal acetylation of the well characterized yeast histone H2A Naa40p substrate, the Naa40p histone H4 substrate remained N-terminally free in human haploid cells specifically deleted for canonical Naa40p27 or 237 amino acid long Naa40 (Naa40L), but expressing Naa40S. Interestingly, human Naa40L and Naa40S displayed differential expression and subcellular localization patterns by exhibiting a principal nuclear and cytoplasmic localization, respectively. Further, since Naa40L was identified as being N-terminally myristoylated and shown to interact with N-myristoyltransferase 1 (NMT1), NMT1 may steer Naa40L nuclear import. Differential interactomics data obtained by biotin-dependent proximity labeling (BioID) further hints to context dependent roles of Naa40p proteoforms. More specifically, with Naa40S representing the main co-translationally acting actor, the interactome of Naa40L was enriched for nucleolar proteins implicated in ribosome biogenesis and the assembly of ribonucleoprotein particles, overall indicating a proteoform-specific segregation of previously reported Naa40p activities. Finally, the yeast histone variant H2A.Z and the transcriptionally regulatory protein Lge1 were identified as novel Naa40p substrates, expanding the restricted substrate repertoire of Naa40p with two additional members and further confirming Lge1 as being the first redundant yNatA and yNatD substrate identified to date.

molecular biology↗

bioRxiv2017

REPARATION: Ribosome Profiling Assisted (Re-)Annotation of Bacterial genomes.

Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence context and often underestimate the complexity of the proteome. We developed REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION), a de novo algorithm that takes advantage of experimental protein translation evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation. REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds based on a growth curve model to screen for spurious ORFs. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel (small) ORFs including variants of previously annotated ORFs. Our predictions were supported by matching mass spectrometry (MS) proteomics data, sequence composition and conservation analysis. REPARATION is unique in that it makes use of experimental translation evidence to perform de novo ORF delineation in bacterial genomes irrespective of the sequence context of the reading frame.

microbiology↗

bioRxiv2016

A Unique Ribosome Signature Reveals Bacterial Translation Initiation Sites

ABSTRCTWhile methods for annotation of genes are increasingly reliable the exact identification of the translation initiation site remains a challenging problem. Since the N-termini of proteins often contain regulatory and targeting information developing a robust method for start site identification is crucial. Ribosome profiling reads show distinct patterns of read length distributions around translation initiation sites. These patterns are typically lost in standard ribosome profiling analysis pipelines, when reads from footprints are adjusted to determine the specific codon being translated. Using these unique signatures we build a model capable of predicting translation initiation sites and demonstrate its high accuracy using N-terminal proteomics. Applying this to prokaryotic samples, we re-annotate translation initiation sites and provide evidence of N-terminal truncations and elongations of annotated coding sequences. These re-annotations are supported by the presence of Shine-Dalgarno sequences, structural and sequence based features and N-terminal peptides. Finally, our model identifies 61 novel genes previously undiscovered in the genome.

bioinformatics↗