Biology subjects

Van der Woude, M. W.

Publications and source records attributed to Van der Woude, M. W..

4 recordsLinked to original sources

bioRxiv2026

The YjfJ protein is the effector of a second PspA/VIPP1 system that is widespread in the Gammaproteobacteria

Maintaining the integrity of the cytoplasmic membrane is essential for bacterial cell survival. Unsurprisingly, prokaryotes have evolved conserved mechanisms by which they sense, maintain, and repair membrane integrity in response to stress. The phage shock protein (Psp) is one such system, understood primarily through work undertaken in the Gammaproteobacterial species Escherichia coli and Yersinia enterocolitica. The system utilises an effector, PspA, alongside accessory proteins that sense stress and recruit PspA to damaged membranes. Homologues of PspA - part of the PspA/VIPP1 family - are found in a variety of bacterial phyla. Although most work in the Gammaproteobacteria has concerned the canonical Psp response, there have been descriptions of non-canonical PspA/VIPP1-containing systems that warrant further genomic analysis. By analysing the PspA/VIPP1 content of a diverse selection of Gammaproteobacterial genomes, we reveal the existence of two phylogenetically distinct subtypes of PspA/VIPP1 proteins, PspA- and YjfJ-like, which are found at similar frequencies. The YjfJ-like proteins are not only a novel subtype of PspA/VIPP1, having their own unique set of accessory proteins, but in some species, such as the ESKAPE pathogen Pseudomonas aeruginosa, comprise the only PspA/VIPP1-containing system. Our study positions the YjfJ-like containing systems on equal footing with the PspA system in terms of their conservation and distribution in the Gammaproteobacteria. This suggests that studies into the biological functions of YjfJ-like proteins would be well-justified from their unique presence in some important human pathogens.

microbiology↗

bioRxiv2025

Itaconate utilisation by the human pathogen Pseudomonas aeruginosa requires uptake via the IctPQM TRAP transporter

Pseudomonas aeruginosa PA01 is one of the major causes of disease persistence and mortality in patients with lung pathologies, relying on various host metabolites as carbon and energy sources for growth. The ict-ich-ccl operon (pa0878, pa0882, pa0883) in PAO1 is required for growth on the host molecule itaconate, a C5-dicarboxylate. However, it is not known how itaconate is taken up into P. aeruginosa. Here we demonstrate that a genetically linked tripartite ATP-independent periplasmic (TRAP) transporter (pa0884-pa0886), which is homologous to the known C4-dicarboxylate binding TRAP system, is essential for growth on itaconate, but not for the closely related C4-dicarboxylate succinate. Using tryptophan fluorescence spectroscopy we demonstrate that the substrate binding protein, IctP (PA0884), binds itaconate, but still retains higher affinity for the related C4-dicarboxylates. The structures of IctP bound to itaconate (1.80 [A]) and succinate (1.75 [A]), revealed an enclosed ligand binding pocket with ion pairing interactions with the ligand carboxylates. The C2 methylene group that is the distinguishing feature of itaconate compared to succinate is accommodated by a unique change in the IctP binding site from a Leu to Val, which distinguishes it from closely related C4-dicarboxylate binding SBPs. Together these data suggest that this transporter, which we name IctPQM, has duplicated from a canonical C4-dicarboxylate transporter and its evolution towards itaconate specificity enables this pathogen to now access a key metabolite for persistence in the host.

microbiology↗

bioRxiv2024

Structural unification of diverse membrane-boundacyltransferases reveals a conserved fold that defines the Transmembrane Acyl Transferase (TmAT) superfamily

The movement of acyl groups across biological membranes is essential for many cellular processes. One major family of proteins catalysing this reaction are the acyl transferase family 3 (AT3) proteins, which form a pore to allow acyl-CoA to penetrate the membrane for transfer onto an extracytosolic acceptor molecule. Recent structures of the sequence-unrelated human heparan--glucosaminide N-acetyltransferase (HGSNAT) support a similar transmembrane acyl-group transfer mechanism. Here we demonstrate that both protein families contain a conserved 10-transmembrane helical fold with high structural and detectable sequence conservation around the acyl-CoA pore, supporting the previously proposed Transmembrane Acyl Transferase (TmAT) protein superfamily. In addition, we identify TmAT proteins, including the human Golgi sialate-O-acetyltransferase (CASD1), the human/fungal PIG-W/GWT1 enzymes and the bacterial vancomycin resistance protein VanTG, where the TmAT domains function has been largely unrecognised. We conclude that the TmAT fold represents an ancient architecture for transmembrane acyl-group transfer with important roles in the dynamic modification of glycans in diverse processes across the three domains of life.

biochemistry↗

bioRxiv2022

A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer

Acylation of diverse carbohydrates occurs across all domains of life and can be catalysed by proteins with a membrane bound acyltransferase-3 (AT3) domain (PF01757). In bacteria, these proteins are essential in processes including symbiosis, resistance to viruses and antimicrobials, and biosynthesis of antibiotics, yet their structure and mechanism is largely unknown. In this study, evolutionary co-variance analysis was used to build a computational model of the structure of a bacterial O-antigen modifying acetyltransferase, OafB. The resulting structure exhibited a novel fold for the AT3 domain, which molecular dynamics simulations demonstrated is stable in the membrane. The AT3 domain contains 10 transmembrane helices arranged to form a large cytoplasmic cavity lined by residues known to be essential for function. Further molecular dynamics simulations support a model where the acyl-coA donor spans the membrane through accessing a pore created by movement of an important loop capping the inner cavity, enabling OafB to present the acetyl group close to the likely catalytic resides on the extracytoplasmic surface. Limited but important interactions with the fused SGNH domain in OafB are identified and modelling suggests this domain is mobile and can both accept acyl-groups from the AT3 and then reach beyond the membrane to reach acceptor substrates. Together this new general model of AT3 function provides a framework for the development of inhibitors that could abrogate critical functions of bacterial pathogens.

biochemistry↗