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Cantrell DA, Urbauer RJB, Kim HW, Woods RJ, Urbauer JL, Wood ZA, West CM. Glycosylation Weakens Skp1 Homodimerization in Toxoplasma gondii by Interrupting a Fuzzy Interaction. Biochemistry 2025; 64:2262-2279. [PMID: 40296701 PMCID: PMC12101541 DOI: 10.1021/acs.biochem.4c00859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Revised: 03/28/2025] [Accepted: 04/22/2025] [Indexed: 04/30/2025]
Abstract
Skp1/Cullin-1/F-Box protein (SCF) complexes represent a major class of E3 ubiquitin ligases responsible for proteomic control throughout eukaryotes. Target specificity is mediated by a large set of F-box proteins (FBPs) whose F-box domains interact with Skp1 in a conserved, well-organized fashion. In the social amoeba Dictyostelium, Skp1 is regulated by oxygen-dependent glycosylation which alters Skp1's FBP interactome and inhibits homodimerization that is mediated in part by an ordered interface which overlaps with that of FBPs. Based on sedimentation velocity experiments, Skp1 from the intracellular pathogen Toxoplasma gondii exhibits a homodimerization Kd comparable to that of a previously measured FBP/Skp1 interaction. Glycosylation of Skp1's disordered C-terminal region (CTR) distal to the ordered homodimer interface significantly weakens Skp1 homodimerization, an effect reproduced by CTR deletion. Replacement with a randomized CTR sequence retains high affinity excluding an extension of the ordered dimer interface. Substitution by poly serine weakens the homodimer to a degree equal to its deletion, indicating a composition dependent effect. The contribution of the CTR to Skp1 homodimerization is canceled by high salt consistent with an electrostatic mechanism. All-atom molecular dynamics simulations suggest that the CTR promotes homodimerization via charge cluster interactions. Taken together, the data indicate that glycosylation weakens homodimerization by disrupting a C-terminal fuzzy interaction that functions in tandem with the ordered dimer interface, thereby freeing Skp1 for FBP binding. Thus, the CTR contributes to Skp1/Skp1 and Skp1/FBP interactions via independent mechanisms that are each influenced by O2, indicating multiple constraints on the evolution of its sequence.
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Affiliation(s)
- Donovan A. Cantrell
- †Department
of Biochemistry and Molecular Biology, ‡Department of Chemistry, §Complex Carbohydrate
Research Center, ∥Center for Tropical and Emerging Diseases, ⊥Center for Molecular Medicine, University of Georgia, Athens, Georgia30602, United States
| | - Ramona J. Bieber Urbauer
- †Department
of Biochemistry and Molecular Biology, ‡Department of Chemistry, §Complex Carbohydrate
Research Center, ∥Center for Tropical and Emerging Diseases, ⊥Center for Molecular Medicine, University of Georgia, Athens, Georgia30602, United States
| | - Hyun W. Kim
- †Department
of Biochemistry and Molecular Biology, ‡Department of Chemistry, §Complex Carbohydrate
Research Center, ∥Center for Tropical and Emerging Diseases, ⊥Center for Molecular Medicine, University of Georgia, Athens, Georgia30602, United States
| | - Robert J. Woods
- †Department
of Biochemistry and Molecular Biology, ‡Department of Chemistry, §Complex Carbohydrate
Research Center, ∥Center for Tropical and Emerging Diseases, ⊥Center for Molecular Medicine, University of Georgia, Athens, Georgia30602, United States
| | - Jeffrey L. Urbauer
- †Department
of Biochemistry and Molecular Biology, ‡Department of Chemistry, §Complex Carbohydrate
Research Center, ∥Center for Tropical and Emerging Diseases, ⊥Center for Molecular Medicine, University of Georgia, Athens, Georgia30602, United States
| | - Zachary A. Wood
- †Department
of Biochemistry and Molecular Biology, ‡Department of Chemistry, §Complex Carbohydrate
Research Center, ∥Center for Tropical and Emerging Diseases, ⊥Center for Molecular Medicine, University of Georgia, Athens, Georgia30602, United States
| | - Christopher M. West
- †Department
of Biochemistry and Molecular Biology, ‡Department of Chemistry, §Complex Carbohydrate
Research Center, ∥Center for Tropical and Emerging Diseases, ⊥Center for Molecular Medicine, University of Georgia, Athens, Georgia30602, United States
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Ng TLC, Hoare MP, Maristany MJ, Wilde EJ, Sneideris T, Huertas J, Agbetiameh BK, Furukawa M, Joseph JA, Knowles TPJ, Collepardo-Guevara R, Itzhaki LS, Kumita JR. Tandem-repeat proteins introduce tuneable properties to engineered biomolecular condensates. Chem Sci 2025:d5sc00903k. [PMID: 40375868 PMCID: PMC12076082 DOI: 10.1039/d5sc00903k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2025] [Accepted: 05/04/2025] [Indexed: 05/18/2025] Open
Abstract
The cell's ability to rapidly partition biomolecules into biomolecular condensates is linked to a diverse range of cellular functions. Understanding how the structural attributes of biomolecular condensates are linked with their biological roles can be facilitated by the development of synthetic condensate systems that can be manipulated in a controllable and predictable way. Here, we design and characterise a tuneable synthetic biomolecular condensate platform fusing modular consensus-designed tetratricopeptide repeat (CTPR) proteins to intrinsically-disordered domains. Trends between the CTPR structural attributes and condensate propensity were recapitulated across different experimental conditions and by in silico modelling, demonstrating that the CTPR domain can systematically affect the condensates in a predictable manner. Moreover, we show that incorporating short binding motifs into the CTPR domain results in specific target-protein recruitment into the condensates. Our model system can be rationally designed in a versatile manner to both tune condensate propensity and endow the condensates with new functions.
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Affiliation(s)
- Tin Long Chris Ng
- Department of Pharmacology, University of Cambridge Tennis Court Road Cambridge CB2 1PD UK
| | - Mateo P Hoare
- Department of Pharmacology, University of Cambridge Tennis Court Road Cambridge CB2 1PD UK
| | - M Julia Maristany
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Department of Physics, University of Cambridge, Cavendish Laboratory Cambridge CB3 0FZ UK
| | - Ellis J Wilde
- Department of Pharmacology, University of Cambridge Tennis Court Road Cambridge CB2 1PD UK
| | - Tomas Sneideris
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Jan Huertas
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Department of Genetics, University of Cambridge, Downing Pl Cambridge CB2 3EH UK
| | - Belinda K Agbetiameh
- Department of Pharmacology, University of Cambridge Tennis Court Road Cambridge CB2 1PD UK
| | - Mona Furukawa
- Department of Pharmacology, University of Cambridge Tennis Court Road Cambridge CB2 1PD UK
| | - Jerelle A Joseph
- Department of Chemical and Biological Engineering, Princeton University Princeton NJ 08544 USA
- Omenn-Darling Bioengineering Institute, Princeton University Princeton NJ 08544 USA
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Department of Physics, University of Cambridge, Cavendish Laboratory Cambridge CB3 0FZ UK
- Department of Genetics, University of Cambridge, Downing Pl Cambridge CB2 3EH UK
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge Tennis Court Road Cambridge CB2 1PD UK
| | - Janet R Kumita
- Department of Pharmacology, University of Cambridge Tennis Court Road Cambridge CB2 1PD UK
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Kidane AK, Rosenfeld JR, Johnston JD, Dubbeldam C, Paraan M, Obermeyer AC. Cationic amino acid identity and net charge influence condensate properties in E. coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.29.646054. [PMID: 40236055 PMCID: PMC11996340 DOI: 10.1101/2025.03.29.646054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Understanding the formation of biomolecular condensates (BMC) in biological systems has proven to be a paradigm shift in our understanding of the subcellular organization of biomacromolecules. From RNA metabolism, stress response mechanisms, and amyloidogenic pathologies, condensates have been implicated to play a role in a myriad of cellular phenomena. Despite their near ubiquity, we still do no wholly understand how the primary sequence of biomolecules influences their biophysical and rheological properties. Here, we aim to understand the impact of primary cationic amino acid composition on the properties of condensates. Using engineered recombinant proteins, we show that the formation and phase boundaries of coacervates formed between proteins and RNA is dependent on the cationic amino acid identity, as well as the net charge of the protein involved in condensation. Despite the equivalent charge between arginine and lysine at physiological pH, arginine has been shown to promote increased encapsulation efficiency and salt stability, as well as reduced protein mobility within condensates. We show that arginine-tagged globular proteins also have a higher salt resistance in vitro when compared to similar lysine-tagged globular proteins. This translates to a cellular context in which arginine tagged proteins promote increased condensate formation in model E. coli cells. We were also able to observe a reduction in the total fluorescent recovery and protein mobility within arginine-based condensates via FRAP. Together, these results suggest that in addition to electrostatic interactions and disorder as the main driving forces of phase separation in biological contexts, the primary sequence and side chain composition of proteins plays a significant role in dictating dynamics of coacervates.
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de Marco A. Recent advances in recombinant production of soluble proteins in E. coli. Microb Cell Fact 2025; 24:21. [PMID: 39815265 PMCID: PMC11736966 DOI: 10.1186/s12934-025-02646-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 01/07/2025] [Indexed: 01/18/2025] Open
Abstract
BACKGROUND E. coli still remains the most commonly used organism to produce recombinant proteins in research labs. This condition is mirrored by the attention that researchers dedicate to understanding the biology behind protein expression, which is then exploited to improve the effectiveness of the technology. This effort is witnessed by an impressive number of publications, and this review aims to organize the most relevant novelties proposed in recent years. RESULTS The examined contributions address several of the known bottlenecks related to recombinant expression in E. coli, such as improved glycosylation pathways, more reliable production of proteins whose folding depends on the formation of disulfide bonds, the possibility of controlling and even benefiting from the formation of aggregates or the need to overcome the dependence of bacteria on antibiotics during bacterial culture. Nevertheless, the majority of the published papers aimed at identifying the conditions for optimal control of the translation process to achieve maximal yields of functional exogenous proteins. CONCLUSIONS Despite community commitment, the critical question of what really is the metabolic burden and how it affects both host metabolism and recombinant protein production remains elusive because some experimental results are contradictory. This contribution aims to offer researchers a tool to orient themselves in this complexity. The new capacities offered by artificial intelligence tools could help clarifying this issue, but the training phase will probably require more systematic experimental approaches to collect sufficiently uniform data.
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Affiliation(s)
- Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Nova Gorica, 5000, Slovenia.
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5
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Warthen JL, Lueckheide MJ. Peptides as Targeting Agents and Therapeutics: A Brief Overview. Biomacromolecules 2024; 25:6923-6935. [PMID: 39445576 DOI: 10.1021/acs.biomac.4c00518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
The controllability and specificity of peptides make them ideal for targeting therapeutic delivery systems and as therapeutic agents that interfere with the essential functions of pathogens and tumors. Peptides can also mimic natural protein structures or parts thereof, agonize receptors, and be conjugated to other molecules that will self-assemble. In this short Review, we discuss research from the last ten years into peptide use in three arenas: the treatment of cancer, the treatment of pathogens, and the targeting of specific organs and organelles. These studies demonstrate the successful application of targeting and therapeutic peptides in vitro and in vivo and show the promising range of applications peptides can have going forward.
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Affiliation(s)
- Jalissa L Warthen
- Adelphi University, 1 South Avenue, Garden City, New York 11530, United States
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6
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Ahn SY, Obermeyer AC. Selectivity of Complex Coacervation in Multiprotein Mixtures. JACS AU 2024; 4:3800-3812. [PMID: 39483238 PMCID: PMC11522905 DOI: 10.1021/jacsau.4c00399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/15/2024] [Accepted: 08/14/2024] [Indexed: 11/03/2024]
Abstract
Liquid-liquid phase separation of biomolecules is increasingly recognized as being relevant to various cellular functions, and complex coacervation of biomacromolecules, particularly proteins, is emerging as a key mechanism for this phenomenon. Complex coacervation is also being explored as a potential protein purification method due to its potential scalability, aqueous operation, and ability to produce a highly concentrated product. However, to date, most studies of complex coacervation have evaluated the phase behavior of a binary mixture of two oppositely charged macromolecules. Therefore, a comprehensive understanding of the phase behavior of complex biological mixtures is yet to be established. To address this, a panel of engineered proteins was designed to allow for quantitative analysis of the complex coacervation of individual proteins within a multicomponent mixture. The behavior of individual proteins was evaluated using a defined mixture of proteins that mimics the charge profile of the Escherichia coli proteome. To allow for the direct quantification of proteins in each phase, spectrally separated fluorescent proteins were used to construct the protein mixture. From this quantitative analysis, we observed that protein coacervation was synchronized in the mixture, which was distinctive from the behavior when each protein was evaluated in a single-protein system. Subtle differences in biophysical properties between the proteins, such as the ionization of individual charged residues and overall charge density, became noticeable in the mixture, which allowed us to elucidate parameters for protein complex coacervation. With this understanding, we successfully designed methods to enrich a range of proteins of interest from a mixture of proteins.
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Affiliation(s)
- So Yeon Ahn
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Allie C. Obermeyer
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
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7
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Miki T, Hashimoto M, Takahashi H, Shimizu M, Nakayama S, Furuta T, Mihara H. De novo designed YK peptides forming reversible amyloid for synthetic protein condensates in mammalian cells. Nat Commun 2024; 15:8503. [PMID: 39424799 PMCID: PMC11489810 DOI: 10.1038/s41467-024-52708-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 09/18/2024] [Indexed: 10/21/2024] Open
Abstract
In mammalian cells, protein condensates underlie diverse cell functions. Intensive synthetic biological research has been devoted to fabricating liquid droplets using de novo peptides/proteins designed from scratch in test tubes or bacterial cells. However, the development of de novo sequences for synthetic droplets forming in eukaryotes is challenging. Here, we report YK peptides, comprising 9-15 residues of alternating repeats of tyrosine and lysine, which form reversible amyloid-like fibrils accompanied by binding with poly-anion species such as ATP. By genetically tagging the YK peptide, superfolder GFPs assemble into artificial liquid-like droplets in living cells. Rational design of the YK system allows fine-tuning of the fluidity and construction of multi-component droplets. The YK system not only facilitates intracellular reconstitution of simplified models for natural protein condensates, but it also provides a toolbox for the systematic creation of droplets with different dynamics and composition for in situ evaluation.
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Affiliation(s)
- Takayuki Miki
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Masahiro Hashimoto
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Hiroki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Masatoshi Shimizu
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Sae Nakayama
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Hisakazu Mihara
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
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8
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Barkley RJR, Crowley JC, Brodrick AJ, Zipfel WR, Parker JSL. Fluorescent protein tags affect the condensation properties of a phase-separating viral protein. Mol Biol Cell 2024; 35:ar100. [PMID: 38809580 PMCID: PMC11244164 DOI: 10.1091/mbc.e24-01-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024] Open
Abstract
Fluorescent protein (FP) tags are extensively used to visualize and characterize the properties of biomolecular condensates despite a lack of investigation into the effects of these tags on phase separation. Here, we characterized the dynamic properties of µNS, a viral protein hypothesized to undergo phase separation and the main component of mammalian orthoreovirus viral factories. Our interest in the sequence determinants and nucleation process of µNS phase separation led us to compare the size and density of condensates formed by FP::µNS to the untagged protein. We found an FP-dependent increase in droplet size and density, which suggests that FP tags can promote µNS condensation. To further assess the effect of FP tags on µNS droplet formation, we fused FP tags to µNS mutants to show that the tags could variably induce phase separation of otherwise noncondensing proteins. By comparing fluorescent constructs with untagged µNS, we identified mNeonGreen as the least artifactual FP tag that minimally perturbed µNS condensation. These results show that FP tags can promote phase separation and that some tags are more suitable for visualizing and characterizing biomolecular condensates with minimal experimental artifacts.
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Affiliation(s)
- Russell J. R. Barkley
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850
| | - Jack C. Crowley
- School of Applied and Engineering Physics, College of Engineering, Cornell University, Ithaca, NY 14850
| | - Andrew J. Brodrick
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850
| | - Warren R. Zipfel
- School of Applied and Engineering Physics, College of Engineering, Cornell University, Ithaca, NY 14850
- Meinig School of Biomedical Engineering, College of Engineering, Cornell University, Ithaca, NY 14850
| | - John S. L. Parker
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850
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9
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Ahn SY, Obermeyer AC. Selectivity of Complex Coacervation in Multi-Protein Mixtures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587643. [PMID: 38617366 PMCID: PMC11014547 DOI: 10.1101/2024.04.02.587643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Liquid-liquid phase separation of biomolecules is increasingly recognized as relevant to various cellular functions, and complex coacervation of biomacromolecules, particularly proteins, is emerging as a key mechanism for this phenomenon. Complex coacervation is also being explored as a potential protein purification method due to its potential scalability, aqueous operation, and ability to produce a highly concentrated product. However, to date most studies of complex coacervation have evaluated the phase behavior of a binary mixture of two oppositely charged macromolecules. Therefore, a comprehensive understanding of the phase behavior of complex biological mixtures has yet to be established. To address this, a panel of engineered proteins was designed to allow for quantitative analysis of the complex coacervation of individual proteins within a multi-component mixture. The behavior of individual proteins was evaluated using a defined mixture of proteins that mimics the charge profile of the E. coli proteome. To allow for direct quantification of proteins in each phase, spectrally separated fluorescent proteins were used to construct the protein mixture. From this quantitative analysis, we observed that the coacervation behavior of individual proteins in the mixture was consistent with each other, which was distinctive from the behavior when each protein was evaluated in a single-protein system. Subtle differences in biophysical properties between the proteins became noticeable in the mixture, which allowed us to elucidate parameters for protein complex coacervation. With this understanding, we successfully designed methods to enrich a range of proteins of interest from a mixture of proteins.
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Affiliation(s)
- So Yeon Ahn
- Department of Chemical Engineering, Columbia University, New York, NY
| | - Allie C Obermeyer
- Department of Chemical Engineering, Columbia University, New York, NY
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10
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Rizvi A, Patterson JP. Liquid-liquid phase separation induced auto-confinement. SOFT MATTER 2024; 20:1978-1982. [PMID: 38363091 DOI: 10.1039/d3sm01617j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Confinement allows macromolecules and biomacromolecules to attain arrangements typically unachievable through conventional self-assembly processes. In the field of block copolymers, confinement has been achieved by preparing thin films and controlled solvent evaporation through the use of emulsions. A significant advantage of the confinement-driven self-assembly process is its ability to enable block copolymers to form particles with complex internal morphologies, which would otherwise be inaccessible. Here, we show that liquid-liquid phase separation (LLPS) can induce confinement during the self-assembly of a model block copolymer system. Since this confinement is driven by the block copolymers' tendency to undergo LLPS, we define this confinement type as auto-confinement. This study adds to the growing understanding of how LLPS influences block copolymer self-assembly and provides a new method to achieve confinement driven self-assembly.
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Affiliation(s)
- Aoon Rizvi
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA.
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA.
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11
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Liao J, Yeong V, Obermeyer AC. Charge-Patterned Disordered Peptides Tune Intracellular Phase Separation in Bacteria. ACS Synth Biol 2024; 13:598-612. [PMID: 38308651 DOI: 10.1021/acssynbio.3c00564] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
Subcellular phase-separated compartments, known as biomolecular condensates, play an important role in the spatiotemporal organization of cells. To understand the sequence-determinants of phase separation in bacteria, we engineered protein-based condensates in Escherichia coli using electrostatic interactions as the main driving force. Minimal cationic disordered peptides were used to supercharge negative, neutral, and positive globular model proteins, enabling their phase separation with anionic biomacromolecules in the cell. The phase behavior was governed by the interaction strength between the cationic proteins and anionic biopolymers, in addition to the protein concentration. The interaction strength primarily depended on the overall net charge of the protein, but the distribution of charge between the globular and disordered domains also had an impact. Notably, the protein charge distribution between domains could tune mesoscale attributes such as the size, number, and subcellular localization of condensates within E. coli cells. The length and charge density of the disordered peptides had significant effects on protein expression levels, ultimately influencing the formation of condensates. Taken together, charge-patterned disordered peptides provide a platform for understanding the molecular grammar underlying phase separation in bacteria.
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Affiliation(s)
- Jane Liao
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Vivian Yeong
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Allie C Obermeyer
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
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12
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Biswas S, Hecht AL, Noble SA, Huang Q, Gillilan RE, Xu AY. Understanding the Impacts of Molecular and Macromolecular Crowding Agents on Protein-Polymer Complex Coacervates. Biomacromolecules 2023; 24:4771-4782. [PMID: 37815312 PMCID: PMC10646951 DOI: 10.1021/acs.biomac.3c00545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/25/2023] [Indexed: 10/11/2023]
Abstract
Complex coacervation refers to the liquid-liquid phase separation (LLPS) process occurring between charged macromolecules. The study of complex coacervation is of great interest due to its implications in the formation of membraneless organelles (MLOs) in living cells. However, the impacts of the crowded intracellular environment on the behavior and interactions of biomolecules involved in MLO formation are not fully understood. To address this knowledge gap, we investigated the effects of crowding on a model protein-polymer complex coacervate system. Specifically, we examined the influence of sucrose as a molecular crowder and polyethylene glycol (PEG) as a macromolecular crowder. Our results reveal that the presence of crowders led to the formation of larger coacervate droplets that remained stable over a 25-day period. While sucrose had a minimal effect on the physical properties of the coacervates, PEG led to the formation of coacervates with distinct characteristics, including higher density, increased protein and polymer content, and a more compact internal structure. These differences in coacervate properties can be attributed to the effects of crowders on individual macromolecules, such as the conformation of model polymers, and nonspecific interactions among model protein molecules. Moreover, our results show that sucrose and PEG have different partition behaviors: sucrose was present in both the coacervate and dilute phases, while PEG was observed to be excluded from the coacervate phase. Collectively, our findings provide insights into the understanding of crowding effects on complex coacervation, shedding light on the formation and properties of coacervates in the context of MLOs.
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Affiliation(s)
- Shanta Biswas
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Alison L Hecht
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Sadie A Noble
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York 14853, United States
| | - Richard E Gillilan
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York 14853, United States
| | - Amy Y Xu
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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