4.8 Review

Synthetic protein condensates for cellular and metabolic engineering

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

LLPSDB v2.0: an updated database of proteins undergoing liquid-liquid phase separation in vitro

Xi Wang et al.

Summary: Emerging evidence suggests that liquid-liquid phase separation (LLPS) of proteins has a crucial role in various biological processes and related diseases. A database called LLPSDB was developed to gather comprehensive data on proteins involved in LLPS and their experimental conditions. The updated version, LLPSDB v2.0, contains more than double the amount of curated data and improved web interface, providing a more comprehensive and helpful resource for users.

BIOINFORMATICS (2022)

Article Biochemical Research Methods

Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells

Mike T. Veling et al.

Summary: Many organisms have the ability to survive extreme conditions and recover to normal life, thanks in part to repetitive, amphipathic, and intrinsically disordered proteins. Through the evaluation of extremotolerance-associated proteins, it has been found that some of them can protect human cells from chemically induced apoptosis. Additionally, a region of the human ApoE protein has been identified with similarities to extremotolerance-associated proteins and also has the ability to protect against apoptosis.

ACS SYNTHETIC BIOLOGY (2022)

Article Chemistry, Multidisciplinary

Small Molecules Modulate Liquid-to-Solid Transitions in Phase-Separated Tau Condensates

Sagun Jonchhe et al.

Summary: This study found that in Tau protein condensates, the halftime of the liquid-to-solid transition is affected by anions' solvation energy according to the Hofmeister series. Charged groups facilitate the transition, similar to the Hofmeister effect, while hydrophobic alkyl chains and aromatic rings inhibit it. These findings not only elucidate the driving force of the liquid-to-solid transition in Tau condensates but also provide guidelines for designing small molecules to modulate this important transition.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2022)

Article Biochemistry & Molecular Biology

Sequence Determinants of the Aggregation of Proteins Within Condensates Generated by Liquid-liquid Phase Separation

Michele Vendruscolo et al.

Summary: This study investigates the sequence determinants of protein aggregation via the condensation pathway and identifies three relevant features: droplet-promoting propensity, aggregation-promoting propensity, and multimodal interactions quantified by the binding mode entropy. By using this approach, aggregation-promoting mutations in droplet-forming proteins associated with amyotrophic lateral sclerosis (ALS) can be predicted.

JOURNAL OF MOLECULAR BIOLOGY (2022)

Article Cell Biology

Material properties of phase-separated TFEB condensates regulate the autophagy-lysosome pathway

Zheng Wang et al.

Summary: The liquid-like condensates of the transcription factor TFEB have low fusion propensity and their material properties can be modified by small molecules.

JOURNAL OF CELL BIOLOGY (2022)

Review Microbiology

Physiological limitations and opportunities in microbial metabolic engineering

Jose Montano Lopez et al.

Summary: Metabolic engineering plays a crucial role in improving the environmental sustainability of transportation and chemical manufacturing sectors by utilizing engineered microorganisms and overcoming physiological challenges. Understanding how host organism's physiological traits impact the performance of engineered metabolic pathways is essential.

NATURE REVIEWS MICROBIOLOGY (2022)

Article Chemistry, Physical

The living interface between synthetic biology and biomaterial design

Allen P. Liu et al.

Summary: Recent advancements in synthetic biology and biomaterials have provided exciting tools for creating new materials and extending the application of synthetic biology. Despite their transformative potential, these fields have mostly progressed separately. This Perspective reviews recent key advances and presents a roadmap for collaboration between the two communities, emphasizing the near-term applications in developing hierarchically structured biomaterials.

NATURE MATERIALS (2022)

Article Multidisciplinary Sciences

Dynamic arrest and aging of biomolecular condensates are modulated by low-complexity domains, RNA and biochemical activity

Miriam Linsenmeier et al.

Summary: In this study, the material properties and aging of biomolecular condensates were analyzed using Differential Dynamic Microscopy (DDM). The results showed that the fluidity of the condensates is regulated by protein domains and structured RNA. Biochemical reactions can maintain the fluid-like properties of the condensates.

NATURE COMMUNICATIONS (2022)

Article Biochemical Research Methods

Rapid regulations of metabolic reactions in Escherichia coli via light-responsive enzyme redistribution

Zikang Huang et al.

Summary: In this study, protein-based condensates were engineered into a photo-activated switch in Escherichia coli (PhASE), enabling the regulation of enzymatic reactions by tuning the spatial correlation of enzymes and substrates. By recruiting enzymes through light-inducible compartments, the reaction rate can be accelerated. This study provides a tool for the study of protein redistribution and reversible regulation of enzymatic reactions in E. coli.

BIOTECHNOLOGY JOURNAL (2022)

Article Multidisciplinary Sciences

Controlling synthetic membraneless organelles by a red-light-dependent singlet oxygen-generating protein

Manjia Li et al.

Summary: This article introduces a method to control the activity of artificial synthetic condensates through light-triggered phase transition. These condensates, similar to membraneless organelles (MLOs), play important roles in biology. With this method, catalysis can be controlled within synthetic MLOs, and the phase transition behavior can be maintained in living cells.

NATURE COMMUNICATIONS (2022)

Article Multidisciplinary Sciences

The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems

Keren Lasker et al.

Summary: Intracellular phase separation is a universal principle for organizing biochemical reactions. The material properties of condensates formed by the protein PopZ in Caulobacter crescentus are determined by a balance between attractive and repulsive forces. Disrupting this balance results in condensates with different material properties. Condensates with specific material properties are important for proper cell division and organismal fitness.

NATURE COMMUNICATIONS (2022)

Article Biophysics

The emergence of phase separation as an organizing principle in bacteria

Christopher A. Azaldegui et al.

Summary: Recent studies in bacteria have shown that membraneless organelles play a crucial role in subcellular organization, but their biochemical functions and assembly mechanisms are not fully understood. Limitations exist in determining the phase of complexes in cells, and gaps remain in our knowledge about the functional role of membraneless organelles in bacteria. Liquid-liquid phase separation is a proposed mechanism for their assembly, and tools like super-resolution microscopy and single-molecule tracking are being explored for further evaluation.

BIOPHYSICAL JOURNAL (2021)

Review Biochemistry & Molecular Biology

Enzymatic Reactions inside Biological Condensates

Yi Zhang et al.

Summary: Biological enzymes accelerate chemical reactions in living organisms, and the complex environment within cells is a major regulator of enzyme activity. Biological condensates, formed spontaneously through phase separation, offer new possibilities for modulating enzymatic reactions.

JOURNAL OF MOLECULAR BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Modularly Built Synthetic Membraneless Organelles Enabling Targeted Protein Sequestration and Release

Masaru Yoshikawa et al.

BIOCHEMISTRY (2021)

Review Biochemistry & Molecular Biology

Synthetic biomolecular condensates to engineer eukaryotic cells

Christopher D. Reinkemeier et al.

Summary: Eukaryotic cells compartmentalize specific functions into specialized organelles, with dynamic biomolecular condensates offering opportunities for synthetic biology. Multiple orthogonally translating organelles have been designed to enable precise protein engineering inside living cells, creating mammalian cells with multiple expanded genetic codes. This provides a pathway to engineer multiple proteins with multiple and distinct functionalities inside living eukaryotes and offers a general strategy toward spatially orthogonal enzyme engineering.

CURRENT OPINION IN CHEMICAL BIOLOGY (2021)

Review Nanoscience & Nanotechnology

Materials design by synthetic biology

Tzu-Chieh Tang et al.

Summary: Synthetic biology utilizes genetic tools to engineer living cells and organisms, similar to machine programming; materials synthetic biology integrates principles from synthetic biology and materials science to redesign living systems into dynamic and responsive materials.

NATURE REVIEWS MATERIALS (2021)

Article Multidisciplinary Sciences

Liquid-liquid phase separation of light-inducible transcription factors increases transcription activation in mammalian cells and mice

Nils Schneider et al.

Summary: The study demonstrates that engineered optogenetic synthetic transcription factors, incorporating intrinsically disordered regions, can form droplets at target promoters and increase gene expression up to fivefold. This approach was effective in multiple mammalian cell lines and in mice.

SCIENCE ADVANCES (2021)

Article Biochemistry & Molecular Biology

Scaffolding protein CcmM directs multiprotein phase separation in β-carboxysome biogenesis

Kun Zang et al.

Summary: Biochemical, biophysical, and structural analysis elucidates how the scaffolding protein CcmM recruits enzymes Rubisco and carbonic anhydrase into a condensate for encapsulation into carboxysomes in cyanobacteria. CcmM, with its distinct domains, plays a central role in mediating pre-carboxysome formation through multivalent interactions, concentrating core components before shell formation. The findings provide insights into carboxysome assembly and its implications in agricultural biotechnology.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

Review Biochemistry & Molecular Biology

Designer Condensates: A Toolkit for the Biomolecular Architect

Renee L. Hastings et al.

Summary: Protein phase separation is a novel paradigm in cell biology that provides insights into how cells compartmentalize biochemical reactions and encode function in liquid-like assemblies. This understanding offers immense opportunities for designing and sculpting biological matter to create new functionalized materials and tools for synthetic biology. Studies suggest that designer condensates have potential applications in industry and medicine.

JOURNAL OF MOLECULAR BIOLOGY (2021)

Article Chemistry, Physical

Biomolecular Condensates: Sequence Determinants of Phase Separation, Microstructural Organization, Enzymatic Activity, and Material Properties

Benjamin S. Schuster et al.

Summary: This perspective article reviews recent advances and challenges in understanding the formation and function of membraneless organelles, emphasizing the diverse molecular organization within biomolecular condensates and the potential impact of liquid-like material properties on enzymatic activity. The need for improved quantitative characterization tools and the development of sequence-structure-dynamics relationships is also discussed.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

Review Cell Biology

Biomolecular condensates at the nexus of cellular stress, protein aggregation disease and ageing

Simon Alberti et al.

Summary: Biomolecular condensates, formed through liquid-liquid phase separation in a tightly regulated manner, have fundamental roles in cellular organization and physiology. Recent studies provide insights into how cellular stress, ageing-related loss of homeostasis, and a decline in protein quality control may contribute to the formation of aberrant, disease-causing condensates.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2021)

Article Cell Biology

Predicting protein condensate formation using machine learning

Guido van Mierlo et al.

Summary: Membraneless organelles are liquid condensates formed through liquid-liquid phase separation, which plays a crucial role in cellular homeostasis. The PSAP machine-learning classifier, based on amino acid content, is effective in predicting phase separation likelihood, serving as a valuable tool for identifying phase separating proteins in health and disease research.

CELL REPORTS (2021)

Article Multidisciplinary Sciences

Programmable viscoelasticity in protein-RNA condensates with disordered sticker-spacer polypeptides

Ibraheem Alshareedah et al.

Summary: The authors demonstrate that disordered polypeptide-RNA condensates exhibit rheological properties similar to that of a viscoelastic Maxwell fluid, and utilize simple polypeptide design rules to create microcondensates with tunable viscoelasticity.

NATURE COMMUNICATIONS (2021)

Article Chemistry, Multidisciplinary

Synthetic Protein Condensates That Inducibly Recruit and Release Protein Activity in Living Cells

Masaru Yoshikawa et al.

Summary: Scientists have successfully constructed synthetic protein condensate systems that can recruit and release proteins in mammalian cells in response to small molecules or light, allowing control over cellular processes and protein activity. This represents a new platform for chemogenetic and optogenetic control of protein activity in mammalian cells, a crucial step towards tailor-made engineering of synthetic protein condensate-based soft materials with various functionalities for biological and biomedical applications.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

Article Multidisciplinary Sciences

Learning the molecular grammar of protein condensates from sequence determinants and embeddings

Kadi L. Saar et al.

Summary: Research has shown that proteins prone to liquid-liquid phase separation are more disordered, less hydrophobic, and have lower Shannon entropy than other protein sequences. By using machine learning models and neural network language models, it is possible to predict and understand protein phase behavior effectively.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Multidisciplinary Sciences

A modular tool to query and inducibly disrupt biomolecular condensates

Carmen N. Hernandez-Candia et al.

Summary: The DisCo method allows for fast, inducible, and specific disruption of tagged condensates in mammalian cells by using chemical dimerizers to induce the recruitment of a ligand into condensates leading to condensate disassembly.

NATURE COMMUNICATIONS (2021)

Article Cell Biology

Generic nature of the condensed states of proteins

Monika Fuxreiter et al.

Summary: Proteins undergoing liquid-liquid phase separation are being discovered more frequently, with the liquid condensed state considered a fundamental state of proteins, playing various biological functions.

NATURE CELL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Designer membraneless organelles sequester native factors for control of cell behavior

Mikael Garabedian et al.

Summary: The subcellular compartmentalization of macromolecules is essential for controlling biochemical reactions by increasing flux and preventing inhibitory interactions. We have developed a synthetic membraneless organelle platform that can control endogenous cellular activities by sequestering and insulating native proteins. By relocalizing targeted enzymes to synthetic condensates, we are able to efficiently regulate cellular behaviors such as proliferation, division, and cytoskeletal organization, and demonstrate strategies for releasing cargo from condensates to switch cells between functional states. These synthetic organelles offer a powerful and versatile approach to controlling cell decision-making in various model systems, with broad applications in cellular engineering.

NATURE CHEMICAL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

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

William Peeples et al.

Summary: Biomolecular condensates concentrate macromolecules into discrete cellular foci without an encapsulating membrane, leading to accelerated reaction rates through increased concentrations and physical organization of molecules. The SUMOylation enzyme cascade can be recruited into droplets generated by liquid-liquid phase separation, significantly increasing reaction rates with substantial specificity among different substrates. This modulation of reaction rates in condensates is achieved through mass action and changes in substrate K-M, likely due to scaffold-induced molecular organization.

NATURE CHEMICAL BIOLOGY (2021)

Editorial Material Cell Biology

The role of ordered cooperative assembly in biomolecular condensates

Elgin Korkmazhan et al.

Summary: This comment emphasizes the role of partial order in biomolecular condensates, suggesting that ordered interactions between condensate components could be key to the formation and function of a variety of partially ordered macromolecular assemblies.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2021)

Review Biochemistry & Molecular Biology

It's not just a phase: function and characteristics of RNA-binding proteins in phase separation

Hannah J. Wiedner et al.

Summary: The organization of RNA in phase-separated condensates provides insights into how sequestration of RNA-binding proteins and RNAs modulates gene expression. This understanding has implications for basic cell biology, the pathogenesis of human diseases, and the development of novel therapies. Biomolecular condensates formed through phase separation play a crucial role in coordinating cellular reactions and regulating various biological phenomena.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

Article Biochemical Research Methods

Localized Proteolysis for the Construction of Intracellular Asymmetry in Escherichia coli

Jui-Chung Hong et al.

Summary: The study shows that localized proteolysis can be employed to construct intracellular asymmetry in Escherichia coli, providing a new strategy for polarization in developmental cell biology. Circuits designed in this study may help to expand the synthetic biology repository for the engineering of synthetic morphogenesis.

ACS SYNTHETIC BIOLOGY (2021)

Review Nanoscience & Nanotechnology

Engineered living biomaterials

Aleixandre Rodrigo-Navarro et al.

Summary: Engineered living materials consist of living cells and polymeric matrices, allowing for controllable responses and dynamic functions. Microorganisms as the active component in these materials can respond to environmental stimuli and have a wide range of biomedical applications.

NATURE REVIEWS MATERIALS (2021)

Review Biotechnology & Applied Microbiology

Synthetic Protein Scaffolding at Biological Membranes

James B. Y. H. Behrendorff et al.

TRENDS IN BIOTECHNOLOGY (2020)

Article Multidisciplinary Sciences

TDP-43 α-helical structure tunes liquid-liquid phase separation and function

Alexander E. Conicella et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Review Biology

Protein assembly systems in natural and synthetic biology

Giulio Chiesa et al.

BMC BIOLOGY (2020)

Review Biochemistry & Molecular Biology

Making the Case for Disordered Proteins and Biomolecular Condensates in Bacteria

Megan C. Cohan et al.

TRENDS IN BIOCHEMICAL SCIENCES (2020)

Article Biochemistry & Molecular Biology

Formation and functionalization of membraneless compartments inEscherichia coli

Shao-Peng Wei et al.

NATURE CHEMICAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Designer protein assemblies with tunable phase diagrams in living cells

Meta Heidenreich et al.

NATURE CHEMICAL BIOLOGY (2020)

Article Chemistry, Multidisciplinary

De novo engineering of intracellular condensates using artificial disordered proteins

Michael Dzuricky et al.

NATURE CHEMISTRY (2020)

Article Multidisciplinary Sciences

Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation

Anne-Marie Ladouceur et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

Tunable multiphase dynamics of arginine and lysine liquid condensates

Rachel S. Fisher et al.

NATURE COMMUNICATIONS (2020)

Review Plant Sciences

Biomolecular condensates in photosynthesis and metabolism

Tobias Wunder et al.

CURRENT OPINION IN PLANT BIOLOGY (2020)

Article Multidisciplinary Sciences

Protein condensates as aging Maxwell fluids

Louise Jawerth et al.

SCIENCE (2020)

Review Biochemistry & Molecular Biology

Drops and fibers - how biomolecular condensates and cytoskeletal filaments influence each other

Tina Wiegand et al.

EMERGING TOPICS IN LIFE SCIENCES (2020)

Article Multidisciplinary Sciences

Small molecules as potent biphasic modulators of protein liquid-liquid phase separation

W. Michael Babinchak et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes

Christopher D. Reinkemeier et al.

SCIENCE (2019)

Article Biochemistry & Molecular Biology

Light-based control of metabolic flux through assembly of synthetic organelles

Evan M. Zhao et al.

NATURE CHEMICAL BIOLOGY (2019)

Article Multidisciplinary Sciences

DEAD-box ATPases are global regulators of phase-separated organelles

Maria Hondele et al.

NATURE (2019)

Article Biochemical Research Methods

Modular Thermal Control of Protein Dimerization

Dan I. Piraner et al.

ACS SYNTHETIC BIOLOGY (2019)

Article Biochemistry & Molecular Biology

First-generation predictors of biological protein phase separation

Robert M. Vernon et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2019)

Review Biochemistry & Molecular Biology

Formation of biological condensates via phase separation: Characteristics, analytical methods, and physiological implications

Zhe Feng et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2019)

Review Biotechnology & Applied Microbiology

Probing and engineering liquid-phase organelles

Dan Bracha et al.

NATURE BIOTECHNOLOGY (2019)

Article Biochemistry & Molecular Biology

Human antibody-based chemically induced dimerizers for cell therapeutic applications

Zachary B. Hill et al.

NATURE CHEMICAL BIOLOGY (2018)

Article Multidisciplinary Sciences

RNA buffers the phase separation behavior of prion-like RNA binding proteins

Shovamayee Maharana et al.

SCIENCE (2018)

Review Biochemistry & Molecular Biology

Organization and Function of Non-dynamic Biomolecular Condensates

Jeffrey B. Woodruff et al.

TRENDS IN BIOCHEMICAL SCIENCES (2018)

Review Cell Biology

Protein Phase Separation: A New Phase in Cell Biology

Steven Boeynaems et al.

TRENDS IN CELL BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli

Elliot Dine et al.

CELL SYSTEMS (2018)

Article Multidisciplinary Sciences

Controllable protein phase separation and modular recruitment to form responsive membraneless organelles

Benjamin S. Schuster et al.

NATURE COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

Yongdae Shin et al.

Article Biochemistry & Molecular Biology

Tunable thermal bioswitches for in vivo control of microbial therapeutics

Dan I. Piraner et al.

NATURE CHEMICAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Near-infrared optogenetic pair for protein regulation and spectral multiplexing

Taras A. Redchuk et al.

NATURE CHEMICAL BIOLOGY (2017)

Article Multidisciplinary Sciences

Direct observation of structure and dynamics during phase separation of an elastomeric protein

Sean E. Reichheld et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Review Multidisciplinary Sciences

Liquid phase condensation in cell physiology and disease

Yongdae Shin et al.

SCIENCE (2017)

Article Biochemistry & Molecular Biology

Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets

Yongdae Shin et al.

Article Biochemical Research Methods

A bacterial phytochrome-based optogenetic system controllable with near-infrared light

Andrii A. Kaberniuk et al.

NATURE METHODS (2016)

Article Multidisciplinary Sciences

Caulobacter PopZ forms an intrinsically disordered hub in organizing bacterial cell poles

Joshua A. Holmes et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Multidisciplinary Sciences

The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics

Shana Elbaum-Garfinkle et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biochemistry & Molecular Biology

The Bacterial Cytoplasm Has Glass-like Properties and Is Fluidized by Metabolic Activity

Bradley R. Parry et al.

Article Multidisciplinary Sciences

An optimized optogenetic clustering tool for probing protein interaction and function

Amir Taslimi et al.

NATURE COMMUNICATIONS (2014)

Article Biochemistry & Molecular Biology

Using Optogenetics to Interrogate the Dynamic Control of Signal Transmission by the Ras/Erk Module

Jared E. Toettcher et al.

Article Biotechnology & Applied Microbiology

Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs

Dokyun Na et al.

NATURE BIOTECHNOLOGY (2013)

Article Biochemical Research Methods

TULIPs: tunable, light-controlled interacting protein tags for cell biology

Devin Strickland et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Spatiotemporal control of gene expression by a light-switchable transgene system

Xue Wang et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Rapid blue-light-mediated induction of protein interactions in living cells

Matthew J. Kennedy et al.

NATURE METHODS (2010)

Article Biotechnology & Applied Microbiology

Synthetic protein scaffolds provide modular control over metabolic flux

John E. Dueber et al.

NATURE BIOTECHNOLOGY (2009)