Intrinsically Disordered Bacterial Polar Organizing Protein Z, PopZ, Interacts with Protein Binding Partners Through an N-terminal Molecular Recognition Feature

Nordyke, Christopher T.; Ahmed, Yasin Mohammed; Puterbaugh, Ryan Z.; Bowman, Grant R.; Varga, Krisztina

doi:10.1016/j.jmb.2020.09.020

Cited by 12 publications

(9 citation statements)

References 101 publications

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“…2a, Supplementary Fig. 2a): (i) a short N-terminal helical region (H1) used for client binding 30,31 , (ii) a 78 amino-acid (aa) IDR (IDR-78) 31 , and (iii) a helical C-terminal region (H2, H3, and H4) which is required for PopZ self-oligomerization 27 . To define the molecular mechanism driving phase separation of PopZ, we examined the contribution of each of these domains to condensation in human and Caulobacter cells.…”

Section: Introductionmentioning

confidence: 99%

A modular platform for engineering function of natural and synthetic biomolecular condensates

Lasker

Boeynaems

et al. 2021

Preprint

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Phase separation is emerging as a universal principle for how cells use dynamic subcompartmentalization to organize biochemical reactions in time and space. Yet, whether the emergent physical properties of these biomolecular condensates are important for their biological function remains unclear. The intrinsically disordered protein PopZ forms membraneless condensates at the poles of the bacterium Caulobacter crescentus and selectively sequesters kinase-signaling cascades to regulate asymmetric cell division. By dissecting the molecular grammar underlying PopZ phase separation, we find that unlike many eukaryotic examples, where unstructured regions drive condensation, a structured domain of PopZ drives condensation, while conserved repulsive features of the disordered region modulate material properties. By generating rationally designed PopZ mutants, we find that the exact material properties of PopZ condensates directly determine cellular fitness, providing direct evidence for the physiological importance of the emergent properties of biomolecular condensates. Our work codifies a clear set of design principles illuminating how sequence variation in a disordered domain alters the function of a widely conserved bacterial condensate. We used these insights to repurpose PopZ as a modular platform for generating synthetic condensates of tunable function in human cells.

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Section: Introductionmentioning

confidence: 99%

A modular platform for engineering function of natural and synthetic biomolecular condensates

Lasker

Boeynaems

et al. 2021

Preprint

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“…Research has shown that IDPs play an increasingly important role in the biology and biochemical pathways of bacteria. For example, the protein Bd0108 is an IDP that regulates pilus secretion and the decision of when to eat other bacteria for Bdellovibrio bacterivorous 32 , a triplet of small IDPs was found to affect flagellum gene expression and motility in Salmonella 52 , and PopZ (polar organizing protein) is an IDP that forms a protein recruitment hub at bacterial poles [53][54] . Our work here now adds Prx to the short but growing list of known bacterial IDPs.…”

Section: Discussionmentioning

confidence: 99%

TheStreptococcusphage protein paratox is an intrinsically disordered protein.

Asakereh,

Rutbeek,

Singh

et al. 2024

Preprint

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The bacteriophage protein paratox blocks quorum sensing in its streptococcal host by directly binding the signal receptor and transcription factor ComR. This reduces ability ofStreptococcusto uptake environmental DNA and protects phage DNA from damage by recombination. Past work characterizing the paratox:ComR molecular interaction revealed that paratox adopts a well-ordered globular fold when bound to ComR. However, solution-state biophysical measurements suggested that paratox may be conformationally dynamic. To address this discrepancy, we investigated the stability and dynamic properties of paratox in solution using circular dichroism, nuclear magnetic resonance, and several fluorescence-based protein folding assays. Our work shows that under dilute buffer conditions paratox is intrinsically disordered. We also show that the addition of kosmotropic salts or protein stabilizing osmolytes induces paratox folding. However, only the addition of ComR was able to induce paratox to adopt its previously characterized globular fold. Furthermore, as we can induce different paratox folding-states we characterize Prx folding thermodynamics and folding kinetics using stopped flow measurements. Based upon the kinetic results, paratox is a highly dynamic protein in dilute solution, folding and refolding within the 10 ms timescale. Overall, our results demonstrate that the streptococcal phage protein paratox is an intrinsically disordered protein in a two-state equilibrium with a solute-stabilized folded form. Furthermore, the solute-stabilized paratox fold is likely the predominant form of paratox in a solute-crowded bacterial cell. Finally, our work suggests that Prx binds and inhibits ComR, and thus quorum sensing inStreptococcus, by a combination of conformational selection and induced-fit binding mechanisms.

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“…PopZ shows many of the characteristic features shared by molecules that form cellular condensates (Banani et al, 2017 ; Nordyke et al, 2020 ; Posey et al, 2018 ; Ptacin et al, 2014 ; Shin & Brangwynne, 2017 ). PopZ is largely disordered.…”

Section: Introductionmentioning

confidence: 99%

“…PopZ is largely disordered. Its N‐terminal region binds clients through a short conserved helix (Holmes et al, 2016 ; Nordyke et al, 2020 ). The central region of PopZ is disordered with many prolines and negatively charged amino acids and likely acts as a tuner of PopZ material properties (Lasker et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Integrative visualization of the molecular structure of a cellular microdomain

Goodsell

Lasker

2023

Protein Science

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An integrative approach to visualization is used to create a visual snapshot of the structural biology of the polar microdomain of Caulobacter crescentus . The visualization is based on the current state of molecular and cellular knowledge of the microdomain and its cellular context. The collaborative process of researching and executing the visualization has identified aspects that are well determined and areas that require further study. The visualization is useful for dissemination, education, and outreach, and the study lays the groundwork for future 3D modeling and simulation of this well‐studied example of a cellular condensate.

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Intrinsically Disordered Bacterial Polar Organizing Protein Z, PopZ, Interacts with Protein Binding Partners Through an N-terminal Molecular Recognition Feature

Cited by 12 publications

References 101 publications

A modular platform for engineering function of natural and synthetic biomolecular condensates

A modular platform for engineering function of natural and synthetic biomolecular condensates

TheStreptococcusphage protein paratox is an intrinsically disordered protein.

Integrative visualization of the molecular structure of a cellular microdomain

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