Mechanistic dissection of increased enzymatic rate in a phase-separated compartment

Peeples, William B.; Rosen, Michael K.

doi:10.1038/s41589-021-00801-x

Cited by 189 publications

(168 citation statements)

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“…Protein/RNA coacervates, spider silk protein, and elastic-like protein were also engineered in E. coli with reversible formations, tunable dynamics, and selective enrichments in components, depending on the protein levels and the ratio of charged residues ( Mushnikov et al, 2019 ; Wei et al, 2020 ; Yeong et al, 2020 ). In a recently engineered condensate comprised of small ubiquitin-like modifier (SUMOylation), enzyme activity increased approximately 36-fold in the droplets (compared with the surrounding bulk solution) ( Peeples and Rosen, 2021 ). These studies have paved the way for the construction of synthetic membraneless organelles with designer functions in prokaryotes.…”

Section: Discussionmentioning

confidence: 99%

Liquid-Liquid Phase Separation: Unraveling the Enigma of Biomolecular Condensates in Microbial Cells

et al. 2021

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Numerous examples of microbial phase-separated biomolecular condensates have now been identified following advances in fluorescence imaging and single molecule microscopy technologies. The structure, function, and potential applications of these microbial condensates are currently receiving a great deal of attention. By neatly compartmentalizing proteins and their interactors in membrane-less organizations while maintaining free communication between these macromolecules and the external environment, microbial cells are able to achieve enhanced metabolic efficiency. Typically, these condensates also possess the ability to rapidly adapt to internal and external changes. The biological functions of several phase-separated condensates in small bacterial cells show evolutionary convergence with the biological functions of their eukaryotic paralogs. Artificial microbial membrane-less organelles are being constructed with application prospects in biocatalysis, biosynthesis, and biomedicine. In this review, we provide an overview of currently known biomolecular condensates driven by liquid-liquid phase separation (LLPS) in microbial cells, and we elaborate on their biogenesis mechanisms and biological functions. Additionally, we highlight the major challenges and future research prospects in studying microbial LLPS.

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Section: Discussionmentioning

confidence: 99%

Liquid-Liquid Phase Separation: Unraveling the Enigma of Biomolecular Condensates in Microbial Cells

et al. 2021

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“…This effect is likely to be most pronounced for reaction cascades, such as transcription, where multiple components must function together to produce a functional outcome. Condensates can also act beyond mass action to control biochemistry, for example by changing the kinetics of molecular interactions [ 49 , 50 ], or the structural organization of enzymes and substrates [ 51 ], or the conformation of enzymes [ 52 ]. However, phase separation can also decrease biological activity by sequestering a protein and thus limiting access to its site of action, or by actively inhibiting it [ 48 ].…”

Section: Discussionmentioning

confidence: 99%

Poly-glutamine-dependent self-association as a potential mechanism for regulation of androgen receptor activity

et al. 2022

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The androgen receptor (AR) plays a central role in prostate cancer. Development of castration resistant prostate cancer (CRPC) requires androgen-independent activation of AR, which involves its large N-terminal domain (NTD) and entails extensive epigenetic changes depending in part on histone lysine demethylases (KDMs) that interact with AR. The AR-NTD is rich in low-complexity sequences, including a polyQ repeat. Longer polyQ sequences were reported to decrease transcriptional activity and to protect against prostate cancer, although they can lead to muscular atrophy. However, the molecular mechanisms underlying these observations are unclear. Using NMR spectroscopy, here we identify weak interactions between the AR-NTD and the KDM4A catalytic domain, and between the AR ligand-binding domain and a central KDM4A region that also contains low-complexity sequences. We also show that the AR-NTD can undergo liquid-liquid phase separation in vitro, with longer polyQ sequences phase separating more readily. Moreover, longer polyQ sequences hinder nuclear localization in the absence of hormone and increase the propensity for formation of AR-containing puncta in the nucleus of cells treated with dihydrotestosterone. These results lead us to hypothesize that polyQ-dependent liquid-liquid phase separation may provide a mechanism to decrease the transcriptional activity of AR, potentially opening new opportunities to design effective therapies against CRPC and muscular atrophy.

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“…As the condensates grow in size at the expense of the accumulation of components, transcription and replication rates would increase at least 1 order of magnitude, as a consequence of the concentration/condensation process [ 127 ] ( Fig 2B ). Such a mass action phenomenon largely increases the effective local concentration of both the polymerase, its nucleocapsid template and the NTP substrates and cofactors, maximizing RNA synthesis, capping, and methylation, resulting in transcription amplification [ 128 ].…”

Section: Biochemical Advantages Of Llps For Viral Factory Formation Function and Fatementioning

confidence: 99%

Deconstructing virus condensation

et al. 2021

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Viruses have evolved precise mechanisms for using the cellular physiological pathways for their perpetuation. These virus-driven biochemical events must be separated in space and time from those of the host cell. In recent years, granular structures, known for over a century for rabies virus, were shown to host viral gene function and were named using terms such as viroplasms, replication sites, inclusion bodies, or viral factories (VFs). More recently, these VFs were shown to be liquid-like, sharing properties with membrane-less organelles driven by liquid–liquid phase separation (LLPS) in a process widely referred to as biomolecular condensation. Some of the best described examples of these structures come from negative stranded RNA viruses, where micrometer size VFs are formed toward the end of the infectious cycle. We here discuss some basic principles of LLPS in connection with several examples of VFs and propose a view, which integrates viral replication mechanisms with the biochemistry underlying liquid-like organelles. In this view, viral protein and RNA components gradually accumulate up to a critical point during infection where phase separation is triggered. This yields an increase in transcription that leads in turn to increased translation and a consequent growth of initially formed condensates. According to chemical principles behind phase separation, an increase in the concentration of components increases the size of the condensate. A positive feedback cycle would thus generate in which crucial components, in particular nucleoproteins and viral polymerases, reach their highest levels required for genome replication. Progress in understanding viral biomolecular condensation leads to exploration of novel therapeutics. Furthermore, it provides insights into the fundamentals of phase separation in the regulation of cellular gene function given that virus replication and transcription, in particular those requiring host polymerases, are governed by the same biochemical principles.

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Mechanistic dissection of increased enzymatic rate in a phase-separated compartment

Cited by 189 publications

References 50 publications

Liquid-Liquid Phase Separation: Unraveling the Enigma of Biomolecular Condensates in Microbial Cells

Liquid-Liquid Phase Separation: Unraveling the Enigma of Biomolecular Condensates in Microbial Cells

Poly-glutamine-dependent self-association as a potential mechanism for regulation of androgen receptor activity

Deconstructing virus condensation

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