1
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Ambadi Thody S, Clements HD, Baniasadi H, Lyon AS, Sigman MS, Rosen MK. Small-molecule properties define partitioning into biomolecular condensates. Nat Chem 2024:10.1038/s41557-024-01630-w. [PMID: 39271915 DOI: 10.1038/s41557-024-01630-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/13/2024] [Indexed: 09/15/2024]
Abstract
Biomolecular condensates regulate cellular function by compartmentalizing molecules without a surrounding membrane. Condensate function arises from the specific exclusion or enrichment of molecules. Thus, understanding condensate composition is critical to characterizing condensate function. Whereas principles defining macromolecular composition have been described, understanding of small-molecule composition remains limited. Here we quantified the partitioning of ~1,700 biologically relevant small molecules into condensates composed of different macromolecules. Partitioning varied nearly a million-fold across compounds but was correlated among condensates, indicating that disparate condensates are physically similar. For one system, the enriched compounds did not generally bind macromolecules with high affinity under conditions where condensates do not form, suggesting that partitioning is not governed by site-specific interactions. Correspondingly, a machine learning model accurately predicts partitioning using only computed physicochemical features of the compounds, chiefly those related to solubility and hydrophobicity. These results suggest that a hydrophobic environment emerges upon condensate formation, driving the enrichment and exclusion of small molecules.
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Affiliation(s)
- Sabareesan Ambadi Thody
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Hanna D Clements
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Hamid Baniasadi
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Andrew S Lyon
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Matthew S Sigman
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA.
| | - Michael K Rosen
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA.
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2
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Ruan K, Bai G, Fang Y, Li D, Li T, Liu X, Lu B, Lu Q, Songyang Z, Sun S, Wang Z, Zhang X, Zhou W, Zhang H. Biomolecular condensates and disease pathogenesis. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1792-1832. [PMID: 39037698 DOI: 10.1007/s11427-024-2661-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/21/2024] [Indexed: 07/23/2024]
Abstract
Biomolecular condensates or membraneless organelles (MLOs) formed by liquid-liquid phase separation (LLPS) divide intracellular spaces into discrete compartments for specific functions. Dysregulation of LLPS or aberrant phase transition that disturbs the formation or material states of MLOs is closely correlated with neurodegeneration, tumorigenesis, and many other pathological processes. Herein, we summarize the recent progress in development of methods to monitor phase separation and we discuss the biogenesis and function of MLOs formed through phase separation. We then present emerging proof-of-concept examples regarding the disruption of phase separation homeostasis in a diverse array of clinical conditions including neurodegenerative disorders, hearing loss, cancers, and immunological diseases. Finally, we describe the emerging discovery of chemical modulators of phase separation.
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Affiliation(s)
- Ke Ruan
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Ge Bai
- Nanhu Brain-computer Interface Institute, Hangzhou, 311100, China.
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Yanshan Fang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 510000, China.
| | - Boxun Lu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai, 200433, China.
| | - Qing Lu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Zhou Songyang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Shuguo Sun
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Zheng Wang
- The Second Affiliated Hospital, School of Basic Medical Sciences, Institute of Biomedical Innovation, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
| | - Xin Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China.
| | - Wen Zhou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Sasazawa M, Tomares DT, Childers WS, Saurabh S. Biomolecular condensates as stress sensors and modulators of bacterial signaling. PLoS Pathog 2024; 20:e1012413. [PMID: 39146259 PMCID: PMC11326607 DOI: 10.1371/journal.ppat.1012413] [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: 08/17/2024] Open
Abstract
Microbes exhibit remarkable adaptability to environmental fluctuations. Signaling mechanisms, such as two-component systems and secondary messengers, have long been recognized as critical for sensing and responding to environmental cues. However, recent research has illuminated the potential of a physical adaptation mechanism in signaling-phase separation, which may represent a ubiquitous mechanism for compartmentalizing biochemistry within the cytoplasm in the context of bacteria that frequently lack membrane-bound organelles. This review considers the broader prospect that phase separation may play critical roles as rapid stress sensing and response mechanisms within pathogens. It is well established that weak multivalent interactions between disordered regions, coiled-coils, and other structured domains can form condensates via phase separation and be regulated by specific environmental parameters in some cases. The process of phase separation itself acts as a responsive sensor, influenced by changes in protein concentration, posttranslational modifications, temperature, salts, pH, and oxidative stresses. This environmentally triggered phase separation can, in turn, regulate the functions of recruited biomolecules, providing a rapid response to stressful conditions. As examples, we describe biochemical pathways organized by condensates that are essential for cell physiology and exhibit signaling features. These include proteins that organize and modify the chromosome (Dps, Hu, SSB), regulate the decay, and modification of RNA (RNase E, Hfq, Rho, RNA polymerase), those involved in signal transduction (PopZ, PodJ, and SpmX) and stress response (aggresomes and polyphosphate granules). We also summarize the potential of proteins within pathogens to function as condensates and the potential and challenges in targeting biomolecular condensates for next-generation antimicrobial therapeutics. Together, this review illuminates the emerging significance of biomolecular condensates in microbial signaling, stress responses, and regulation of cell physiology and provides a framework for microbiologists to consider the function of biomolecular condensates in microbial adaptation and response to diverse environmental conditions.
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Affiliation(s)
- Moeka Sasazawa
- Department of Chemistry, New York University, New York, New York, United States of America
| | - Dylan T Tomares
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - W Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Saumya Saurabh
- Department of Chemistry, New York University, New York, New York, United States of America
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4
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Guo Y, Zhang X. Unveiling intracellular phase separation: advances in optical imaging of biomolecular condensates. Trends Biochem Sci 2024:S0968-0004(24)00163-4. [PMID: 39034215 DOI: 10.1016/j.tibs.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
Intracellular biomolecular condensates, which form via phase separation, display a highly organized ultrastructure and complex properties. Recent advances in optical imaging techniques, including super-resolution microscopy and innovative microscopic methods that leverage the intrinsic properties of the molecules observed, have transcended the limitations of conventional microscopies. These advances facilitate the exploration of condensates at finer scales and in greater detail. The deployment of these emerging but sophisticated imaging tools allows for precise observations of the multiphasic organization and physicochemical properties of these condensates, shedding light on their functions in cellular processes. In this review, we highlight recent progress in methodological innovations and their profound implications for understanding the organization and dynamics of intracellular biomolecular condensates.
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Affiliation(s)
- Yinfeng Guo
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, PR China
| | - Xin Zhang
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, PR China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, PR China.
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5
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Kelley FM, Ani A, Pinlac EG, Linders B, Favetta B, Barai M, Ma Y, Singh A, Dignon GL, Gu Y, Schuster BS. Controlled and orthogonal partitioning of large particles into biomolecular condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603072. [PMID: 39071308 PMCID: PMC11275771 DOI: 10.1101/2024.07.11.603072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Biomolecular condensates arising from liquid-liquid phase separation contribute to diverse cellular processes, such as gene expression. Partitioning of client molecules into condensates is critical to regulating the composition and function of condensates. Previous studies suggest that client size limits partitioning, with dextrans >5 nm excluded from condensates. Here, we asked whether larger particles, such as macromolecular complexes, can partition into condensates based on particle-condensate interactions. We sought to discover the biophysical principles that govern particle inclusion in or exclusion from condensates using polymer nanoparticles with tailored surface chemistries as models of macromolecular complexes. Particles coated with polyethylene glycol (PEG) did not partition into condensates. We next leveraged the PEGylated particles as an inert platform to which we conjugated specific adhesive moieties. Particles functionalized with biotin partitioned into condensates containing streptavidin, driven by high-affinity biotin-streptavidin binding. Oligonucleotide-decorated particles exhibited varying degrees of partitioning into condensates, depending on condensate composition. Partitioning of oligonucleotide-coated particles was tuned by altering salt concentration, oligonucleotide length, and oligonucleotide surface density. Remarkably, beads with distinct surface chemistries partitioned orthogonally into immiscible condensates. Based on our experiments, we conclude that arbitrarily large particles can controllably partition into biomolecular condensates given sufficiently strong condensate-particle interactions, a conclusion also supported by our coarse-grained molecular dynamics simulations and theory. These findings may provide insights into how various cellular processes are achieved based on partitioning of large clients into biomolecular condensates, as well as offer design principles for the development of drug delivery systems that selectively target disease-related biomolecular condensates.
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Affiliation(s)
- Fleurie M. Kelley
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
| | - Anas Ani
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
| | - Emily G. Pinlac
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
| | - Bridget Linders
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
| | - Bruna Favetta
- Department of Biomedical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
| | - Mayur Barai
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
| | - Yuchen Ma
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
| | - Arjun Singh
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
| | - Gregory L. Dignon
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
| | - Yuwei Gu
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
| | - Benjamin S. Schuster
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
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6
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Guo X, Farag M, Qian N, Yu X, Ni A, Ma Y, Yu W, King MR, Liu V, Lee J, Zare RN, Min W, Pappu RV, Dai Y. Biomolecular condensates can function as inherent catalysts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602359. [PMID: 39026887 PMCID: PMC11257451 DOI: 10.1101/2024.07.06.602359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
We report the discovery that chemical reactions such as ATP hydrolysis can be catalyzed by condensates formed by intrinsically disordered proteins (IDPs), which themselves lack any intrinsic ability to function as enzymes. This inherent catalytic feature of condensates derives from the electrochemical environments and the electric fields at interfaces that are direct consequences of phase separation. The condensates we studied were capable of catalyzing diverse hydrolysis reactions, including hydrolysis and radical-dependent breakdown of ATP whereby ATP fully decomposes to adenine and multiple carbohydrates. This distinguishes condensates from naturally occurring ATPases, which can only catalyze the dephosphorylation of ATP. Interphase and interfacial properties of condensates can be tuned via sequence design, thus enabling control over catalysis through sequence-dependent electrochemical features of condensates. Incorporation of hydrolase-like synthetic condensates into live cells enables activation of transcriptional circuits that depend on products of hydrolysis reactions. Inherent catalytic functions of condensates, which are emergent consequences of phase separation, are likely to affect metabolic regulation in cells.
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Affiliation(s)
- Xiao Guo
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Naixin Qian
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Xia Yu
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Anton Ni
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Yuefeng Ma
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Wen Yu
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Matthew R. King
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Vicky Liu
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Joonho Lee
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Rohit V. Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Yifan Dai
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
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7
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Davis MC, André AAM, Kjaergaard M. Entering the Next Phase: Predicting Biological Effects of Biomolecular Condensates. J Mol Biol 2024:168645. [PMID: 38848869 DOI: 10.1016/j.jmb.2024.168645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Biomolecular condensates are increasingly recognized as important drivers of cellular function; their dysregulation leads to pathology and disease. We discuss three questions in terms of the impending utility of data-driven techniques to predict condensate-driven biological outcomes, i.e., the impact of cellular state changes on condensates, the effect of condensates on biochemical processes within, and condensate properties that result in cellular dysregulation and disease.
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Affiliation(s)
- Maria C Davis
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alain A M André
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; The Danish Research Institute for Translational Neuroscience (DANDRITE), Denmark.
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8
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Yang J, Chung CI, Koach J, Liu H, Navalkar A, He H, Ma Z, Zhao Q, Yang X, He L, Mittag T, Shen Y, Weiss WA, Shu X. MYC phase separation selectively modulates the transcriptome. Nat Struct Mol Biol 2024:10.1038/s41594-024-01322-6. [PMID: 38811792 DOI: 10.1038/s41594-024-01322-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/22/2024] [Indexed: 05/31/2024]
Abstract
Dysregulation and enhanced expression of MYC transcription factors (TFs) including MYC and MYCN contribute to the majority of human cancers. For example, MYCN is amplified up to several hundredfold in high-risk neuroblastoma. The resulting overexpression of N-myc aberrantly activates genes that are not activated at low N-myc levels and drives cell proliferation. Whether increasing N-myc levels simply mediates binding to lower-affinity binding sites in the genome or fundamentally changes the activation process remains unclear. One such activation mechanism that could become important above threshold levels of N-myc is the formation of aberrant transcriptional condensates through phase separation. Phase separation has recently been linked to transcriptional regulation, but the extent to which it contributes to gene activation remains an open question. Here we characterized the phase behavior of N-myc and showed that it can form dynamic condensates that have transcriptional hallmarks. We tested the role of phase separation in N-myc-regulated transcription by using a chemogenetic tool that allowed us to compare non-phase-separated and phase-separated conditions at equivalent N-myc levels, both of which showed a strong impact on gene expression compared to no N-myc expression. Interestingly, we discovered that only a small percentage (<3%) of N-myc-regulated genes is further modulated by phase separation but that these events include the activation of key oncogenes and the repression of tumor suppressors. Indeed, phase separation increases cell proliferation, corroborating the biological effects of the transcriptional changes. However, our results also show that >97% of N-myc-regulated genes are not affected by N-myc phase separation, demonstrating that soluble complexes of TFs with the transcriptional machinery are sufficient to activate transcription.
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Affiliation(s)
- Junjiao Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Chan-I Chung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Jessica Koach
- Departments of Neurology, Neurological Surgery, Pediatrics, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Hongjiang Liu
- Institute for Human Genetics, Departments of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Ambuja Navalkar
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao He
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Zhimin Ma
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Qian Zhao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaoyu Yang
- Institute for Human Genetics, Departments of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Liang He
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yin Shen
- Institute for Human Genetics, Departments of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - William A Weiss
- Departments of Neurology, Neurological Surgery, Pediatrics, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Center, University of California, San Francisco, San Francisco, CA, USA.
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9
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Kilgore HR, Chinn I, Mikhael PG, Mitnikov I, Van Dongen C, Zylberberg G, Afeyan L, Banani S, Wilson-Hawken S, Lee TI, Barzilay R, Young RA. Protein codes promote selective subcellular compartmentalization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589616. [PMID: 38659952 PMCID: PMC11042338 DOI: 10.1101/2024.04.15.589616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must efficiently assemble. Here, we demonstrate that proteins with shared functions share amino acid sequence codes that guide them to compartment destinations. A protein language model, ProtGPS, was developed that predicts with high performance the compartment localization of human proteins excluded from the training set. ProtGPS successfully guided generation of novel protein sequences that selectively assemble in targeted subcellular compartments. ProtGPS also identified pathological mutations that change this code and lead to altered subcellular localization of proteins. Our results indicate that protein sequences contain not only a folding code, but also a previously unrecognized code governing their distribution in specific cellular compartments.
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Affiliation(s)
- Henry R. Kilgore
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Itamar Chinn
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter G. Mikhael
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ilan Mitnikov
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Guy Zylberberg
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lena Afeyan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Salman Banani
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Susana Wilson-Hawken
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Program of Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Regina Barzilay
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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10
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Zhu L, Pan Y, Hua Z, Liu Y, Zhang X. Ionic Effect on the Microenvironment of Biomolecular Condensates. J Am Chem Soc 2024; 146:14307-14317. [PMID: 38722189 DOI: 10.1021/jacs.4c04036] [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: 05/23/2024]
Abstract
Biomolecules such as proteins and RNA could organize to form condensates with distinct microenvironments through liquid-liquid phase separation (LLPS). Recent works have demonstrated that the microenvironment of biomolecular condensates plays a crucial role in mediating biological activities, such as the partition of biomolecules, and the subphase organization of the multiphasic condensates. Ions could influence the phase transition point of LLPS, following the Hofmeister series. However, the ion-specific effect on the microenvironment of biomolecular condensates remains unknown. In this study, we utilized fluorescence lifetime imaging microscopy (FLIM), fluorescence recovery after photobleaching (FRAP), and microrheology techniques to investigate the ion effect on the microenvironment of condensates. We found that ions significantly affect the microenvironment of biomolecular condensates: salting-in ions increase micropolarity and reduce the microviscosity of the condensate, while salting-out ions induce opposing effects. Furthermore, we manipulate the miscibility and multilayering behavior of condensates through ion-specific effects. In summary, our work provides the first quantitative survey of the microenvironment of protein condensates in the presence of ions from the Hofmeister series, demonstrating how ions impact micropolarity, microviscosity, and viscoelasticity of condensates. Our results bear implications on how membrane-less organelles would exhibit varying microenvironments in the presence of continuously changing cellular conditions.
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Affiliation(s)
- Longchen Zhu
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, P. R. China
| | - Yifei Pan
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, P. R. China
| | - Ziyi Hua
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Xin Zhang
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, P. R. China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, P. R. China
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11
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Sun X, Zhou Y, Wang Z, Peng M, Wei X, Xie Y, Wen C, Liu J, Ye M. Biomolecular Condensates Decipher Molecular Codes of Cell Fate: From Biophysical Fundamentals to Therapeutic Practices. Int J Mol Sci 2024; 25:4127. [PMID: 38612940 PMCID: PMC11012904 DOI: 10.3390/ijms25074127] [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: 02/29/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Cell fate is precisely modulated by complex but well-tuned molecular signaling networks, whose spatial and temporal dysregulation commonly leads to hazardous diseases. Biomolecular condensates (BCs), as a newly emerging type of biophysical assemblies, decipher the molecular codes bridging molecular behaviors, signaling axes, and clinical prognosis. Particularly, physical traits of BCs play an important role; however, a panoramic view from this perspective toward clinical practices remains lacking. In this review, we describe the most typical five physical traits of BCs, and comprehensively summarize their roles in molecular signaling axes and corresponding major determinants. Moreover, establishing the recent observed contribution of condensate physics on clinical therapeutics, we illustrate next-generation medical strategies by targeting condensate physics. Finally, the challenges and opportunities for future medical development along with the rapid scientific and technological advances are highlighted.
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Affiliation(s)
- Xing Sun
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Yangyang Zhou
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Zhiyan Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Menglan Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Xianhua Wei
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Yifang Xie
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Chengcai Wen
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Jing Liu
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
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Liu J, Cabral H, Mi P. Nanocarriers address intracellular barriers for efficient drug delivery, overcoming drug resistance, subcellular targeting and controlled release. Adv Drug Deliv Rev 2024; 207:115239. [PMID: 38437916 DOI: 10.1016/j.addr.2024.115239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/16/2024] [Accepted: 02/27/2024] [Indexed: 03/06/2024]
Abstract
The cellular barriers are major bottlenecks for bioactive compounds entering into cells to accomplish their biological functions, which limits their biomedical applications. Nanocarriers have demonstrated high potential and benefits for encapsulating bioactive compounds and efficiently delivering them into target cells by overcoming a cascade of intracellular barriers to achieve desirable therapeutic and diagnostic effects. In this review, we introduce the cellular barriers ahead of drug delivery and nanocarriers, as well as summarize recent advances and strategies of nanocarriers for increasing internalization with cells, promoting intracellular trafficking, overcoming drug resistance, targeting subcellular locations and controlled drug release. Lastly, the future perspectives of nanocarriers for intracellular drug delivery are discussed, which mainly focus on potential challenges and future directions. Our review presents an overview of intracellular drug delivery by nanocarriers, which may encourage the future development of nanocarriers for efficient and precision drug delivery into a wide range of cells and subcellular targets.
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Affiliation(s)
- Jing Liu
- Department of Radiology, Huaxi MR Research Center (HMRRC), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17 South Renmin Road, Chengdu, Sichuan 610041, China
| | - Horacio Cabral
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Peng Mi
- Department of Radiology, Huaxi MR Research Center (HMRRC), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17 South Renmin Road, Chengdu, Sichuan 610041, China.
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13
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Ansari AZ. In search of chemical rationales. Nat Chem Biol 2024; 20:264-265. [PMID: 38030787 DOI: 10.1038/s41589-023-01488-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Affiliation(s)
- Aseem Z Ansari
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN, USA.
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Sood A, Zhang B. Preserving condensate structure and composition by lowering sequence complexity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569249. [PMID: 38076908 PMCID: PMC10705451 DOI: 10.1101/2023.11.29.569249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Biological condensates play a vital role in organizing cellular chemistry. They selectively partition biomolecules, preventing unwanted cross-talk and buffering against chemical noise. Intrinsically disordered proteins (IDPs) serve as primary components of these condensates due to their flexibility and ability to engage in multivalent, non-specific interactions, leading to spontaneous aggregation. Theoretical advancements are critical at connecting IDP sequences with condensate emergent properties to establish the so-called molecular grammar. We proposed an extension to the stickers and spacers model, incorporating non-specific pairwise interactions between spacers alongside specific interactions among stickers. Our investigation revealed that while spacer interactions contribute to phase separation and co-condensation, their non-specific nature leads to disorganized condensates. Specific sticker-sticker interactions drive the formation of condensates with well-defined structures and molecular composition. We discussed how evolutionary pressures might emerge to affect these interactions, leading to the prevalence of low complexity domains in IDP sequences. These domains suppress spurious interactions and facilitate the formation of biologically meaningful condensates.
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Affiliation(s)
- Amogh Sood
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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