ATP-responsive biomolecular condensates tune bacterial kinase signaling

Saurabh, Saumya; Chong, Trisha N.; Bayas, Camille; Dahlberg, Peter D.; Cartwright, Heather; Moerner, W. E.; Shapiro, Lucy

doi:10.1126/sciadv.abm6570

Cited by 46 publications

(50 citation statements)

References 60 publications

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“…The ability to avoid dissolution at high levels of ADP is in contrast to observations by Saurabh et al . that showed that ATP could dissolve SpmX biomolecular condensates at concentrations at and above 2 mM 31 . This suggests that biomolecular condensation phase diagrams display varying robustness to ATP.…”

Section: Resultsmentioning

confidence: 99%

“…These membraneless compartments organize ABC transporters 10 , single-stranded (ss) DNA-binding proteins 11 , aggresomes 12 , cell division protein FtsZ 13 , BapA amyloid biofilm matrix protein 14 , circadian rhythm associated proteins 15 and carboxysomes 16 . For example, in Caulobacter crescentus , two compositionally distinct biomolecular condensates regulate a network of signaling proteins to promote asymmetric cell division 17, 18, 19 . It has been shown that histidine kinases can be regulated spatially by sensory domain stimulation 17 .…”

Section: Introductionmentioning

confidence: 99%

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RNase E biomolecular condensates stimulate PNPase activity

Collins

Tomares

Schrader

et al. 2022

Preprint

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Bacterial Ribonucleoprotein bodies (BR-bodies) play an essential role in organizing RNA degradation via liquid-liquid phase separation in the cytoplasm of bacteria. BR-bodies mediate multi-step mRNA decay through the concerted activity of the endoribonuclease RNase E coupled with the 3'-5' exonuclease Polynucleotide Phosphorylase (PNPase). Our past in vivo studies indicated that the loss of PNPase recruitment into BR-bodies led to a significant build-up of RNA decay intermediates in Caulobacter crescentus. We reconstituted RNase E's C-terminal domain together with PNPase to understand how RNase E biomolecular condensates can tailor the functions of PNPase. We found that PNPase catalytic activity is accelerated when colocalized with the RNase E biomolecular condensates. In contrast, disruption of the RNase E-PNPase protein-protein interaction led to a loss of PNPase recruitment into the BR-bodies and a loss of ribonuclease rate enhancement. We also found that BR-bodies could enhance the decay of select RNA substrates, as we observed a 3.4-fold enhancement of polyadenylic acid (poly(A)) degradation and no impact upon poly(U) degradation. Our investigation into the origins of the 3.4-fold rate enhancement for poly(A) decay indicates a combination of scaffolding and mass action effects impact due to the concentrated biomolecular condensate environment accelerating RNA decay. Consistent with our past in vivo work, these studies suggest BR-bodies are sites of accelerated RNA decay that can shape the available transcriptome.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

RNase E biomolecular condensates stimulate PNPase activity

Collins

Tomares

Schrader

et al. 2022

Preprint

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“…PopZ is prone to self-associating into higher-ordered dense clusters that form microdomains at the cell poles, which allow the entry of several proteins but exclude larger macromolecules, such as ribosomes or chromosomal DNA [ 55 ]. Recently, fluorescence microscopy analyses revealed that PopZ formed condensates with a spherical morphology in vitro and that IDRs of the protein molecule were necessary and sufficient for condensate formation [ 56 ]. The same authors noticed that the phase behavior of PopZ condensates was a function of protein and salt concentration.…”

Section: Bacterial Proteins With a Potential Propensity For Liquid–li...mentioning

confidence: 99%

Getting Closer to Decrypting the Phase Transitions of Bacterial Biomolecules

et al. 2022

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Liquid–liquid phase separation (LLPS) of biomolecules has emerged as a new paradigm in cell biology, and the process is one proposed mechanism for the formation of membraneless organelles (MLOs). Bacterial cells have only recently drawn strong interest in terms of studies on both liquid-to-liquid and liquid-to-solid phase transitions. It seems that these processes drive the formation of prokaryotic cellular condensates that resemble eukaryotic MLOs. In this review, we present an overview of the key microbial biomolecules that undergo LLPS, as well as the formation and organization of biomacromolecular condensates within the intracellular space. We also discuss the current challenges in investigating bacterial biomacromolecular condensates. Additionally, we highlight a summary of recent knowledge about the participation of bacterial biomolecules in a phase transition and provide some new in silico analyses that can be helpful for further investigations.

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“…In many cases, these structures provide a basis for controlling chemical reactions or are themselves affect by reactions. Examples include chemically fueled assemblies [9][10][11][12] and membrane-less compartments that control reactions in biological cells [13][14][15][16], which are also often regulated using chemical modifications of the involved biomolecules [16][17][18][19][20][21]. In fact, chemically controlled droplets might explain how cells originated at the origin of life [22][23][24].…”

Section: Introductionmentioning

confidence: 99%

The intertwined physics of active chemical reactions and phase separation

Zwicker

2022

Preprint

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Phase separation is the thermodynamic process that explains how droplets form in multicomponent fluids. These droplets can provide controlled compartments to localize chemical reactions, and reactions can also affect the droplets' dynamics. This review focuses on the tight interplay between phase separation and chemical reactions originating from thermodynamic constraints. In particular, simple mass action kinetics cannot describe chemical reactions since phase separation requires non-ideal fluids. Instead, thermodynamics implies that passive chemical reactions reduce the complexity of phase diagrams and provide only limited control over the system's behavior. However, driven chemical reactions, which use external energy input to create spatial fluxes, can circumvent thermodynamic constraints. Such active systems can suppress the typical droplet coarsening, control droplet size, and localize droplets. This review provides an extensible framework for describing active chemical reactions in phase separating systems, which forms a basis for improving control in technical applications and understanding self-organized structures in biological cells.

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ATP-responsive biomolecular condensates tune bacterial kinase signaling

Cited by 46 publications

References 60 publications

RNase E biomolecular condensates stimulate PNPase activity

RNase E biomolecular condensates stimulate PNPase activity

Getting Closer to Decrypting the Phase Transitions of Bacterial Biomolecules

The intertwined physics of active chemical reactions and phase separation

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