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4. The SPARC complex defines RNAPII promoters in Trypanosoma brucei

Author

Staneva, Desislava P, primary, Bresson, Stefan, additional, Auchynnikava, Tatsiana, additional, Spanos, Christos, additional, Rappsilber, Juri, additional, Jeyaprakash, A Arockia, additional, Tollervey, David, additional, Matthews, Keith R, additional, and Allshire, Robin C, additional

Published
2022
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7. The SPARC complex defines RNAPII promoters in Trypanosoma brucei

Author

Staneva, Desislava P., primary, Bresson, Stefan, additional, Auchynnikava, Tatsiana, additional, Spanos, Christos, additional, Rappsilber, Juri, additional, Jeyaprakash, A. Arockia, additional, Tollervey, David, additional, Matthews, Keith R., additional, and Allshire, Robin C., additional

Published
2022
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9. The assembly of a GTPase-kinase signalling complex by a bacterial catalytic scaffold

Author

Selyunin, Andrey S., Sutton, Sarah E., Weigele, Bethany A., Reddick, L. Evan, Orchard, Robert C., Bresson, Stefan M., Tomchick, Diana R., and Alto, Neal M.

Subjects
Bacterial proteins -- Properties -- Physiological aspects -- Research -- Health aspects, Cellular signal transduction -- Research -- Health aspects -- Physiological aspects, DNA binding proteins -- Physiological aspects -- Health aspects -- Research, Guanosine triphosphatase -- Physiological aspects -- Health aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The fidelity and specificity of information flow within a cell is controlled by scaffolding proteins that assemble and link enzymes into signalling circuits (1,2). These circuits can be inhibited by bacterial effector proteins that post-translationally modify individual pathway components (3-6). However, there is emerging evidence that pathogens directly organize higher-order signalling networks through enzyme scaffolding (7,8), and the identity of the effectors and their mechanisms of action are poorly understood. Here we identify the enterohaemorrhagic Escherichia coli O157:H7 type III effector EspG as a regulator of endomembrane trafficking using a functional screen, and report ADP-ribosylation factor (ARF) GTPases and p21-activated kinases (PAKs) as its relevant host substrates. The 2.5 A crystal structure of EspG in complex with ARF6 shows how EspG blocks GTPase-activating-protein-assisted GTP hydrolysis, revealing a potent mechanism of GTPase signalling inhibition at organelle membranes. In addition, the 2.8 Å crystal structure of EspG in complex with the autoinhibitory Iα3-helix of PAK2 defines a previously unknown catalytic site in EspG and provides an allosteric mechanism of kinase activation by a bacterial effector. Unexpectedly, ARF and PAKs are organized on adjacent surfaces of EspG, indicating its role as a 'catalytic scaffold' that effectively reprograms cellular events through the functional assembly of GTPase-kinase signalling complex., To identify new signalling pathways targetedby bacterial pathogens, we used a human growth hormone (hGH) secretion assay (9) to measure the ability of type III and type IV effector proteins [...]

Published
2011
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15. Defining the RNA interactome by total RNA‐associated protein purification

Author

Shchepachev, Vadim, Bresson, Stefan, Spanos, Christos, Petfalski, Elisabeth, Fischer, Lutz, Rappsilber, Juri, and Tollervey, David

Subjects
Medicine (General), Saccharomyces cerevisiae Proteins, RNA binding sites, QH301-705.5, Escherichia coli Proteins, Method, Post-translational Modifications, Proteolysis & Proteomics, RNA-Binding Proteins, Methods & Resources, Saccharomyces cerevisiae, yeast, RNA Biology, Thiouracil, Cross-Linking Reagents, R5-920, Ribonucleoproteins, Methods, Escherichia coli, RNA, protein–RNA interaction, phase separation, Biology (General), mass spectrometry
Abstract

The RNA binding proteome (RBPome) was previously investigated using UV crosslinking and purification of poly(A)‐associated proteins. However, most cellular transcripts are not polyadenylated. We therefore developed total RNA‐associated protein purification (TRAPP) based on 254 nm UV crosslinking and purification of all RNA–protein complexes using silica beads. In a variant approach (PAR‐TRAPP), RNAs were labelled with 4‐thiouracil prior to 350 nm crosslinking. PAR‐TRAPP in yeast identified hundreds of RNA binding proteins, strongly enriched for canonical RBPs. In comparison, TRAPP identified many more proteins not expected to bind RNA, and this correlated strongly with protein abundance. Comparing TRAPP in yeast and E. coli showed apparent conservation of RNA binding by metabolic enzymes. Illustrating the value of total RBP purification, we discovered that the glycolytic enzyme enolase interacts with tRNAs. Exploiting PAR‐TRAPP to determine the effects of brief exposure to weak acid stress revealed specific changes in late 60S ribosome biogenesis. Furthermore, we identified the precise sites of crosslinking for hundreds of RNA–peptide conjugates, using iTRAPP, providing insights into potential regulation. We conclude that TRAPP is a widely applicable tool for RBPome characterization.

Published
2019

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