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Contreras‐Llano LE, Liu Y, Henson T, Meyer CC, Baghdasaryan O, Khan S, Lin C, Wang A, Hu CJ, Tan C. Engineering Cyborg Bacteria Through Intracellular Hydrogelation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204175. [PMID: 36628538 PMCID: PMC10037956 DOI: 10.1002/advs.202204175] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/18/2022] [Indexed: 05/06/2023]
Abstract
Natural and artificial cells are two common chassis in synthetic biology. Natural cells can perform complex tasks through synthetic genetic constructs, but their autonomous replication often causes safety concerns for biomedical applications. In contrast, artificial cells based on nonreplicating materials, albeit possessing reduced biochemical complexity, provide more defined and controllable functions. Here, for the first time, the authors create hybrid material-cell entities termed Cyborg Cells. To create Cyborg Cells, a synthetic polymer network is assembled inside each bacterium, rendering them incapable of dividing. Cyborg Cells preserve essential functions, including cellular metabolism, motility, protein synthesis, and compatibility with genetic circuits. Cyborg Cells also acquire new abilities to resist stressors that otherwise kill natural cells. Finally, the authors demonstrate the therapeutic potential by showing invasion into cancer cells. This work establishes a new paradigm in cellular bioengineering by exploiting a combination of intracellular man-made polymers and their interaction with the protein networks of living cells.
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Affiliation(s)
| | - Yu‐Han Liu
- Institute of Biomedical SciencesAcademia SinicaTaipei11529Taiwan
| | - Tanner Henson
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
- Department of SurgeryUniversity of CaliforniaDavis School of MedicineSacramentoCA95817USA
| | - Conary C. Meyer
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
| | | | - Shahid Khan
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
| | - Chi‐Long Lin
- Institute of Biomedical SciencesAcademia SinicaTaipei11529Taiwan
| | - Aijun Wang
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
- Department of SurgeryUniversity of CaliforniaDavis School of MedicineSacramentoCA95817USA
| | - Che‐Ming J. Hu
- Institute of Biomedical SciencesAcademia SinicaTaipei11529Taiwan
| | - Cheemeng Tan
- Department of Biomedical EngineeringUniversity of CaliforniaDavisCA95616USA
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de Castro RJA, Rêgo MTAM, Brandão FS, Pérez ALA, De Marco JL, Poças-Fonseca MJ, Nichols C, Alspaugh JA, Felipe MSS, Alanio A, Bocca AL, Fernandes L. Engineered Fluorescent Strains of Cryptococcus neoformans: a Versatile Toolbox for Studies of Host-Pathogen Interactions and Fungal Biology, Including the Viable but Nonculturable State. Microbiol Spectr 2022; 10:e0150422. [PMID: 36005449 PMCID: PMC9603711 DOI: 10.1128/spectrum.01504-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/05/2022] [Indexed: 12/31/2022] Open
Abstract
Cryptococcus neoformans is an opportunistic fungal pathogen known for its remarkable ability to infect and subvert phagocytes. This ability provides survival and persistence within the host and relies on phenotypic plasticity. The viable but nonculturable (VBNC) phenotype was recently described in C. neoformans, whose study is promising in understanding the pathophysiology of cryptococcosis. The use of fluorescent strains is improving host interaction research, but it is still underexploited. Here, we fused histone H3 or the poly(A) binding protein (Pab) to enhanced green fluorescent protein (eGFP) or mCherry, obtaining a set of C. neoformans transformants with different colors, patterns of fluorescence, and selective markers (hygromycin B resistance [Hygr] or neomycin resistance [Neor]). We validated their similarity to the parental strain in the stress response, the expression of virulence-related phenotypes, mating, virulence in Galleria mellonella, and survival within murine macrophages. PAB-GFP, the brightest transformant, was successfully applied for the analysis of phagocytosis by flow cytometry and fluorescence microscopy. Moreover, we demonstrated that an engineered fluorescent strain of C. neoformans was able to generate VBNC cells. GFP-tagged Pab1, a key regulator of the stress response, evidenced nuclear retention of Pab1 and the assembly of cytoplasmic stress granules, unveiling posttranscriptional mechanisms associated with dormant C. neoformans cells. Our results support that the PAB-GFP strain is a useful tool for research on C. neoformans. IMPORTANCE Cryptococcus neoformans is a human-pathogenic yeast that can undergo a dormant state and is responsible for over 180,000 deaths annually worldwide. We engineered a set of fluorescent transformants to aid in research on C. neoformans. A mutant with GFP-tagged Pab1 improved fluorescence-based techniques used in host interaction studies. Moreover, this mutant induced a viable but nonculturable phenotype and uncovered posttranscriptional mechanisms associated with dormant C. neoformans. The experimental use of fluorescent mutants may shed light on C. neoformans-host interactions and fungal biology, including dormant phenotypes.
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Affiliation(s)
- Raffael Júnio Araújo de Castro
- Laboratory of Applied Immunology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasília, Federal District, Brazil
- CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses et Antifongiques, Institut Pasteur, Paris, France
| | - Marco Túlio Aidar Mariano Rêgo
- Laboratory of Applied Immunology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasília, Federal District, Brazil
| | - Fabiana S. Brandão
- Faculty of Health Science, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasília, Federal District, Brazil
| | - Ana Laura Alfonso Pérez
- Department of Cell Biology, Institute of Biological Sciences, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasilia, Federal District, Brazil
| | - Janice Lisboa De Marco
- Department of Cell Biology, Institute of Biological Sciences, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasilia, Federal District, Brazil
| | - Marcio José Poças-Fonseca
- Department of Genetics and Morphology, Institute of Biological Sciences, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasília, Federal District, Brazil
| | - Connie Nichols
- Duke University School of Medicine, Department of Medicine, Durham, North Carolina, USA
| | - J. Andrew Alspaugh
- Duke University School of Medicine, Department of Medicine, Durham, North Carolina, USA
| | - Maria Sueli S. Felipe
- Catholic University of Brasilia, Campus Asa Norte, Asa Norte, Brasília, Federal District, Brazil
| | - Alexandre Alanio
- CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses et Antifongiques, Institut Pasteur, Paris, France
- Laboratoire de Mycologie et Parasitologie, AP-HP, Hôpital Saint Louis, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Anamélia Lorenzetti Bocca
- Laboratory of Applied Immunology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasília, Federal District, Brazil
| | - Larissa Fernandes
- Laboratory of Applied Immunology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasília, Federal District, Brazil
- Faculty of Ceilândia, Campus UnB Ceilândia, University of Brasília, Ceilândia Sul, Brasília, Federal District, Brazil
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Zimmerli CE, Allegretti M, Rantos V, Goetz SK, Obarska-Kosinska A, Zagoriy I, Halavatyi A, Hummer G, Mahamid J, Kosinski J, Beck M. Nuclear pores dilate and constrict in cellulo. Science 2021; 374:eabd9776. [PMID: 34762489 DOI: 10.1126/science.abd9776] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Christian E Zimmerli
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Matteo Allegretti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vasileios Rantos
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany.,EMBL Hamburg, 22607 Hamburg, Germany
| | - Sara K Goetz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Agnieszka Obarska-Kosinska
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,EMBL Hamburg, 22607 Hamburg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | | | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany.,EMBL Hamburg, 22607 Hamburg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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Daignan-Fornier B, Laporte D, Sagot I. Quiescence Through the Prism of Evolution. Front Cell Dev Biol 2021; 9:745069. [PMID: 34778256 PMCID: PMC8586652 DOI: 10.3389/fcell.2021.745069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/11/2021] [Indexed: 01/13/2023] Open
Abstract
Being able to reproduce and survive is fundamental to all forms of life. In primitive unicellular organisms, the emergence of quiescence as a reversible proliferation arrest has most likely improved cell survival under unfavorable environmental conditions. During evolution, with the repeated appearances of multicellularity, several aspects of unicellular quiescence were conserved while new quiescent cell intrinsic abilities arose. We propose that the formation of a microenvironment by neighboring cells has allowed disconnecting quiescence from nutritional cues. In this new context, non-proliferative cells can stay metabolically active, potentially authorizing the emergence of new quiescent cell properties, and thereby favoring cell specialization. Through its co-evolution with cell specialization, quiescence may have been a key motor of the fascinating diversity of multicellular complexity.
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Jacquel B, Aspert T, Laporte D, Sagot I, Charvin G. Monitoring single-cell dynamics of entry into quiescence during an unperturbed life cycle. eLife 2021; 10:73186. [PMID: 34723791 PMCID: PMC8594939 DOI: 10.7554/elife.73186] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/15/2021] [Indexed: 12/14/2022] Open
Abstract
The life cycle of microorganisms is associated with dynamic metabolic transitions and complex cellular responses. In yeast, how metabolic signals control the progressive choreography of structural reorganizations observed in quiescent cells during a natural life cycle remains unclear. We have developed an integrated microfluidic device to address this question, enabling continuous single-cell tracking in a batch culture experiencing unperturbed nutrient exhaustion to unravel the coordination between metabolic and structural transitions within cells. Our technique reveals an abrupt fate divergence in the population, whereby a fraction of cells is unable to transition to respiratory metabolism and undergoes a reversible entry into a quiescence-like state leading to premature cell death. Further observations reveal that nonmonotonous internal pH fluctuations in respiration-competent cells orchestrate the successive waves of protein superassemblies formation that accompany the entry into a bona fide quiescent state. This ultimately leads to an abrupt cytosolic glass transition that occurs stochastically long after proliferation cessation. This new experimental framework provides a unique way to track single-cell fate dynamics over a long timescale in a population of cells that continuously modify their ecological niche.
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Affiliation(s)
- Basile Jacquel
- Department of Developmental Biology and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Théo Aspert
- Department of Developmental Biology and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Damien Laporte
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France, Bordeaux, France
| | - Isabelle Sagot
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France, Bordeaux, France
| | - Gilles Charvin
- Department of Developmental Biology and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
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6
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Membraneless organelles: phasing out of equilibrium. Emerg Top Life Sci 2021; 4:331-342. [PMID: 32744309 DOI: 10.1042/etls20190190] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/12/2020] [Accepted: 07/15/2020] [Indexed: 12/17/2022]
Abstract
Over the past years, liquid-liquid phase separation (LLPS) has emerged as a ubiquitous principle of cellular organization implicated in many biological processes ranging from gene expression to cell division. The formation of biological condensates, like the nucleolus or stress granules, by LLPS is at its core a thermodynamic equilibrium process. However, life does not operate at equilibrium, and cells have evolved multiple strategies to keep condensates in a non-equilibrium state. In this review, we discuss how these non-equilibrium drivers counteract solidification and potentially detrimental aggregation, and at the same time enable biological condensates to perform work and control the flux of substrates and information in a spatial and temporal manner.
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Abstract
Environmental fluctuations are a common challenge for single-celled organisms; enteric bacteria such as Escherichia coli experience dramatic changes in nutrient availability, pH, and temperature during their journey into and out of the host. While the effects of altered nutrient availability on gene expression and protein synthesis are well known, their impacts on cytoplasmic dynamics and cell morphology have been largely overlooked. Here, we discover that depletion of utilizable nutrients results in shrinkage of E. coli's inner membrane from the cell wall. Shrinkage was accompanied by an ∼17% reduction in cytoplasmic volume and a concurrent increase in periplasmic volume. Inner membrane retraction after sudden starvation occurred almost exclusively at the new cell pole. This phenomenon was distinct from turgor-mediated plasmolysis and independent of new transcription, translation, or canonical starvation-sensing pathways. Cytoplasmic dry-mass density increased during shrinkage, suggesting that it is driven primarily by loss of water. Shrinkage was reversible: upon a shift to nutrient-rich medium, expansion started almost immediately at a rate dependent on carbon source quality. A robust entry into and recovery from shrinkage required the Tol-Pal system, highlighting the importance of envelope coupling during shrinkage and recovery. Klebsiella pneumoniae also exhibited shrinkage when shifted to carbon-free conditions, suggesting a conserved phenomenon. These findings demonstrate that even when Gram-negative bacterial growth is arrested, cell morphology and physiology are still dynamic.
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Britton S, Alber M, Cannon WR. Enzyme activities predicted by metabolite concentrations and solvent capacity in the cell. J R Soc Interface 2020; 17:20200656. [PMID: 33050777 PMCID: PMC7653389 DOI: 10.1098/rsif.2020.0656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/17/2020] [Indexed: 12/23/2022] Open
Abstract
Experimental measurements or computational model predictions of the post-translational regulation of enzymes needed in a metabolic pathway is a difficult problem. Consequently, regulation is mostly known only for well-studied reactions of central metabolism in various model organisms. In this study, we use two approaches to predict enzyme regulation policies and investigate the hypothesis that regulation is driven by the need to maintain the solvent capacity in the cell. The first predictive method uses a statistical thermodynamics and metabolic control theory framework while the second method is performed using a hybrid optimization-reinforcement learning approach. Efficient regulation schemes were learned from experimental data that either agree with theoretical calculations or result in a higher cell fitness using maximum useful work as a metric. As previously hypothesized, regulation is herein shown to control the concentrations of both immediate and downstream product concentrations at physiological levels. Model predictions provide the following two novel general principles: (1) the regulation itself causes the reactions to be much further from equilibrium instead of the common assumption that highly non-equilibrium reactions are the targets for regulation; and (2) the minimal regulation needed to maintain metabolite levels at physiological concentrations maximizes the free energy dissipation rate instead of preserving a specific energy charge. The resulting energy dissipation rate is an emergent property of regulation which may be represented by a high value of the adenylate energy charge. In addition, the predictions demonstrate that the amount of regulation needed can be minimized if it is applied at the beginning or branch point of a pathway, in agreement with common notions. The approach is demonstrated for three pathways in the central metabolism of E. coli (gluconeogenesis, glycolysis-tricarboxylic acid (TCA) and pentose phosphate-TCA) that each require different regulation schemes. It is shown quantitatively that hexokinase, glucose 6-phosphate dehydrogenase and glyceraldehyde phosphate dehydrogenase, all branch points of pathways, play the largest roles in regulating central metabolism.
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Affiliation(s)
- Samuel Britton
- Department of Mathematics, University of California Riverside, Riverside, CA 92505, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92505, USA
| | - Mark Alber
- Department of Mathematics, University of California Riverside, Riverside, CA 92505, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92505, USA
| | - William R. Cannon
- Department of Mathematics, University of California Riverside, Riverside, CA 92505, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92505, USA
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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