Dynamic interplay between the periplasmic chaperone SurA and the BAM complex in outer membrane protein folding

Schiffrin, Bob; Machin, Jonathan; Karamanos, Theodoros K.; Zhuravleva, Anastasia; Brockwell, David J.; Radford, Sheena E.; Calabrese, Antonio N.

doi:10.1038/s42003-022-03502-w

Cited by 19 publications

(9 citation statements)

References 117 publications

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“…SurA plays an important role in facilitating the recruitment of unfolded OMPs from the periplasm to the BAM complex (68). Both our BAM-SurA model and a recently published study using an orthogonal approach to ours (69) place SurA in the same position to simultaneously interact with BamA, BamB, and BamE (Fig. 4D left).…”

Section: Outer Membrane β-Barrel Assembly Machinery Of P Aeruginosa A...mentioning

confidence: 58%

Essential and virulence-related protein interactions of pathogens revealed through deep learning

Humphreys,

Zhang,

Baek

et al. 2024

Preprint

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Identification of bacterial protein protein interactions and predicting the structures of the complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here, we developed a deep learning based pipeline that leverages residue-residue coevolution and protein structure prediction to systematically identify and structurally characterize protein protein interactions at the proteome wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from posttranscriptional modification to acid neutralization to outer membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.

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Section: Outer Membrane β-Barrel Assembly Machinery Of P Aeruginosa A...mentioning

confidence: 58%

Essential and virulence-related protein interactions of pathogens revealed through deep learning

Humphreys,

Zhang,

Baek

et al. 2024

Preprint

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“…48,49 However, the function of SurA is thought to be linked to the BAM complex as evidenced by genetic and structural interactions between SurA and BAM. 48,59 Additionally, recent literature supports a model where SurA binds extended conformations of uOMPs using localized and regulated binding regions, 10,11,15,60,61 leading to a weaker binding in the high nM to low μM range. 13,54,55 Quick client binding and release combined with a proposed interaction with and rate enhancement of BAM may explain why SurA can improve OMP folding in the presence of BAM but has little to no intrinsic ability to improve OMP folding efficiency by itself.…”

Section: Discussionmentioning

confidence: 83%

FkpA Enhances Membrane Protein Folding using an Extensive Interaction Surface

Devlin

Marx

Roskopf

et al. 2022

Preprint

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Outer membrane protein (OMP) biogenesis in gram-negative bacteria is managed by a network of periplasmic chaperones that includes SurA, Skp, and FkpA. These chaperones bind unfolded OMPs (uOMPs) in dynamic conformational ensembles to suppress uOMP aggregation, facilitate diffusion across the periplasm, and enhance OMP folding. FkpA primarily responds to heat-shock stress, but its mechanism is comparatively understudied. To determine FkpA chaperone function, we monitored the folding of a cognate client uOmpA171and found that FkpA increases the folded uOmpA171population but also slows the folding rate, dual functions distinct from the other periplasmic chaperones. The results indicate that FkpA behaves as a chaperone and not as a folding catalyst to directly influence the uOmpA171folding trajectory. We determine the binding affinity between FkpA and uOmpA171by globally fitting sedimentation velocity titrations and found it to be intermediate between the known affinities of Skp and SurA for uOMP clients. Notably, complex formation steeply depends on the urea concentration, suggestive of an extensive binding interface. Initial characterizations of the complex using photo-crosslinking indicates that the binding interface spans the inner surfaces of the entire FkpA molecule. In contrast to prior findings, folding and binding experiments performed using subdomain constructs of FkpA demonstrate that the full-length chaperone is required for full activity. Together these results support that FkpA has a distinct and direct effect on uOMP folding and that it achieves this by utilizing an extensive chaperone-client interface.

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“…This result in itself is somewhat surprising as SurA is thought to be the most important periplasmic chaperone in the OMP biogenesis pathway based on its phenotypic growth defect and the decrease in folded OMP levels upon SurA deletion (Lazar et al, 1998;Sklar et al, 2007). However, the function of SurA is thought to be linked to the BAM complex as evidenced by genetic and structural interactions between SurA and BAM (Schiffrin et al, 2022;Sklar et al, 2007). Additionally, recent literature supports a model where SurA binds extended conformations of uOMPs using localized and regulated binding regions (Calabrese et al, 2020;Jia et al, 2020;Marx et al, 2020aMarx et al, , 2020bSoltes et al, 2016), leading to a weaker binding in the high nM to low μM range (Bitto and McKay, 2003;Schiffrin et al, 2017;Wu et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

FkpA enhances membrane protein folding using an extensive interaction surface

et al. 2023

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Outer membrane protein (OMP) biogenesis in gram‐negative bacteria is managed by a network of periplasmic chaperones that includes SurA, Skp, and FkpA. These chaperones bind unfolded OMPs (uOMPs) in dynamic conformational ensembles to suppress aggregation, facilitate diffusion across the periplasm, and enhance folding. FkpA primarily responds to heat‐shock stress, but its mechanism is comparatively understudied. To determine FkpA chaperone function in the context of OMP folding, we monitored the folding of three OMPs and found that FkpA, unlike other periplasmic chaperones, increases the folded yield but decreases the folding rate of OMPs. The results indicate that FkpA behaves as a chaperone and not as a folding catalyst to influence the OMP folding trajectory. Consistent with the folding assay results, FkpA binds all three uOMPs as determined by sedimentation velocity (SV) and photo‐crosslinking experiments. We determine the binding affinity between FkpA and uOmpA171 by globally fitting SV titrations and find it to be intermediate between the known affinities of Skp and SurA for uOMP clients. Notably, complex formation steeply depends on the urea concentration, suggesting an extensive binding interface. Initial characterizations of the complex using photo‐crosslinking indicate that the binding interface spans the entire FkpA molecule. In contrast to prior findings, folding and binding experiments performed using subdomain constructs of FkpA demonstrate that the full‐length chaperone is required for full activity. Together these results support that FkpA has a distinct and direct effect on OMP folding that it achieves by utilizing an extensive chaperone‐client interface to tightly bind clients.

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Dynamic interplay between the periplasmic chaperone SurA and the BAM complex in outer membrane protein folding

Cited by 19 publications

References 117 publications

Essential and virulence-related protein interactions of pathogens revealed through deep learning

Essential and virulence-related protein interactions of pathogens revealed through deep learning

FkpA Enhances Membrane Protein Folding using an Extensive Interaction Surface

FkpA enhances membrane protein folding using an extensive interaction surface

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