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Sutcliffe EI, Irvine A, Rooney J, Smith D, Northcote HM, McKenzie D, Bakshi S, Nisbet AJ, Price D, Graham R, Morphew R, Atkinson L, Mousley A, Cantacessi C. Antimicrobial peptides in nematode secretions - Unveiling biotechnological opportunities for therapeutics and beyond. Biotechnol Adv 2025; 81:108572. [PMID: 40154760 DOI: 10.1016/j.biotechadv.2025.108572] [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: 12/06/2024] [Revised: 03/02/2025] [Accepted: 03/25/2025] [Indexed: 04/01/2025]
Abstract
Gastrointestinal (GI) parasitic nematodes threaten food security and affect human health and animal welfare globally. Current anthelmintics for use in humans and livestock are challenged by continuous re-infections and the emergence and spread of multidrug resistance, underscoring an urgent need to identify novel control targets for therapeutic exploitation. Recent evidence has highlighted the occurrence of complex interplay between GI parasitic nematodes of humans and livestock and the resident host gut microbiota. Antimicrobial peptides (AMPs) found within nematode biofluids have emerged as potential effectors of these interactions. This review delves into the occurrence, structure, and function of nematode AMPs, highlighting their potential as targets for drug discovery and development. We argue that an integrated approach combining advanced analytical techniques, scalable production methods, and innovative experimental models is needed to unlock the full potential of nematode AMPs and pave the way for the discovery and development of sustainable parasite control strategies.
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Affiliation(s)
- E I Sutcliffe
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - A Irvine
- School of Biological Sciences, Queen's University Belfast, United Kingdom
| | - J Rooney
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - D Smith
- Moredun Research Institute, United Kingdom
| | - H M Northcote
- Department of Life Sciences, Aberystwyth University, United Kingdom
| | - D McKenzie
- School of Biological Sciences, Queen's University Belfast, United Kingdom
| | - S Bakshi
- Department of Engineering, University of Cambridge, United Kingdom
| | - A J Nisbet
- Moredun Research Institute, United Kingdom
| | - D Price
- Moredun Research Institute, United Kingdom
| | - R Graham
- School of Biological Sciences, Queen's University Belfast, United Kingdom
| | - R Morphew
- Department of Life Sciences, Aberystwyth University, United Kingdom
| | - L Atkinson
- School of Biological Sciences, Queen's University Belfast, United Kingdom
| | - A Mousley
- School of Biological Sciences, Queen's University Belfast, United Kingdom
| | - C Cantacessi
- Department of Veterinary Medicine, University of Cambridge, United Kingdom.
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2
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Chen S, Wang Y, Da Zhou, Hu J. Bayesian Inference of Phenotypic Plasticity of Cancer Cells Based on Dynamic Model for Temporal Cell Proportion Data. Biom J 2025; 67:e70055. [PMID: 40298362 DOI: 10.1002/bimj.70055] [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: 06/15/2024] [Revised: 09/18/2024] [Accepted: 10/31/2024] [Indexed: 04/30/2025]
Abstract
Mounting evidence underscores the prevalent hierarchical organization of cancer tissues. At the foundation of this hierarchy reside cancer stem cells, a subset of cells endowed with the pivotal role of engendering the entire cancer tissue through cell differentiation. In recent times, substantial attention has been directed toward the phenomenon of cancer cell plasticity, where the dynamic interconversion between cancer stem cells and nonstem cancer cells has garnered significant interest. Since the task of detecting cancer cell plasticity from empirical data remains a formidable challenge, we propose a Bayesian statistical framework designed to infer phenotypic plasticity within cancer cells, utilizing temporal data on cancer stem cell proportions. Our approach is grounded in a stochastic model, adept at capturing the dynamic behaviors of cells. Leveraging Bayesian analysis, we scrutinize the moment equation governing cancer stem cell proportions, derived from the Kolmogorov forward equation of our stochastic model. Our methodology introduces an improved Euler method for parameter estimation within nonlinear ordinary differential equation models, also extending insights to compositional data. Extensive simulations robustly validate the efficacy of our proposed method. To further corroborate our findings, we apply our approach to analyze published data from SW620 colon cancer cell lines. Our results harmonize with in situ experiments, thereby reinforcing the utility of our method in discerning and quantifying phenotypic plasticity within cancer cells.
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Affiliation(s)
- Shuli Chen
- School of Mathematics, Sun Yat-sen University, Guangzhou, Guangdong, China
- School of Mathematical Science, Xiamen University, Xiamen, Fujian, China
| | - Yuman Wang
- School of Mathematical Science, Xiamen University, Xiamen, Fujian, China
| | - Da Zhou
- School of Mathematical Science, Xiamen University, Xiamen, Fujian, China
| | - Jie Hu
- School of Mathematical Science, Xiamen University, Xiamen, Fujian, China
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3
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Vareschi S, Jaut V, Vijay S, Allen RJ, Schreiber F. Antimicrobial efflux and biofilms: an interplay leading to emergent resistance evolution. Trends Microbiol 2025:S0966-842X(25)00123-4. [PMID: 40410028 DOI: 10.1016/j.tim.2025.04.012] [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: 02/11/2025] [Revised: 04/15/2025] [Accepted: 04/16/2025] [Indexed: 05/25/2025]
Abstract
The biofilm mode of growth and drug efflux are both important factors that impede the treatment of bacterial infections with antimicrobials. Decades of work have uncovered the mechanisms involved in both efflux and biofilm-mediated antimicrobial tolerance, but links between these phenomena have only recently been discovered. Novel findings show how efflux impacts global cellular physiology and antibiotic tolerance, underpinned by phenotypic heterogeneity. In addition efflux can mediate cell-to-cell interactions, relevant in biofilms, via mechanisms including efflux of signaling molecules and metabolites, signaling using pump components and the establishment of local antibiotic gradients via pumping. These recent findings suggest that biofilm antibiotic tolerance and efflux are closely coupled, with synergistic effects leading to the evolution of antimicrobial resistance in the biofilm environment.
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Affiliation(s)
- Silvia Vareschi
- Theoretical Microbial Ecology, Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Valerie Jaut
- Division Biodeterioration and Reference Organisms, Department of Materials and the Environment, Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Srinivasan Vijay
- Theoretical Microbial Ecology, Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Rosalind J Allen
- Theoretical Microbial Ecology, Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
| | - Frank Schreiber
- Division Biodeterioration and Reference Organisms, Department of Materials and the Environment, Federal Institute for Materials Research and Testing, Berlin, Germany
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4
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Alnahhas RN, Andreani V, Dunlop MJ. Evaluating the predictive power of combined gene expression dynamics from single cells on antibiotic survival. mSystems 2025:e0158824. [PMID: 40391890 DOI: 10.1128/msystems.01588-24] [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: 11/23/2024] [Accepted: 04/16/2025] [Indexed: 05/22/2025] Open
Abstract
Heteroresistance and persistence are examples of mechanisms that can allow otherwise drug-susceptible bacteria to survive and resume growth after antibiotic exposure. These temporary forms of antibiotic tolerance can be caused by the upregulation of stress response genes or a decrease in cell growth rate. However, it is not clear how the expression of multiple genes contributes to tolerance phenotypes. Using fluorescent reporters for stress-related genes, we conducted real-time measurements of expression prior to, during, and after antibiotic exposure. We first identified relationships between growth rate and reporter levels based on auto- and cross-correlation analysis, revealing consistent patterns where changes in growth rate were anticorrelated with fluorescence following a delay. We then used pairs of stress gene reporters and time-lapse fluorescence microscopy to measure the growth rate and reporter levels in cells that survived or died following antibiotic exposure. Using these data, we asked whether combined information about reporter expression and growth rate could improve our ability to predict whether a cell would survive or die following antibiotic exposure. We developed a Bayesian inference model to predict how the combination of dual reporter expression levels and growth rate impacts ciprofloxacin survival in Escherichia coli. We found clear evidence of the impact of growth rate and gadX promoter activity on survival. Unexpectedly, our results also revealed examples where additional information from multiple genes decreased prediction accuracy, highlighting an important and underappreciated effect that can occur when integrating data from multiple simultaneous measurements.IMPORTANCETransient increases in bacterial antibiotic tolerance can result in treatment failure despite an infection initially presenting as susceptible, presenting a significant challenge in antibiotic therapy. This phenomenon can also provide a window of opportunity for bacteria to acquire permanent genetic resistance mutations. Although understanding the underlying mechanisms of these antibiotic tolerance phenotypes is crucial for developing effective approaches to treatment, current approaches for studying these transient phenotypes have limitations. Here, we use fluorescent reporters to monitor the expression of genes involved in stress response over time, aiming to link expression with antibiotic survival outcomes. Our results reveal a counterintuitive finding: monitoring multiple gene reporters does not necessarily improve our ability to predict antibiotic survival outcomes compared to single gene reporters. This result emphasizes the need for a deeper mechanistic understanding of the relationship between stress response gene expression and antibiotic tolerance.
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Affiliation(s)
- Razan N Alnahhas
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Virgile Andreani
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
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5
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Nieto C, Vargas-García CA, Singh A. A generalized adder for cell size homeostasis: Effects on stochastic clonal proliferation. Biophys J 2025; 124:1376-1386. [PMID: 40119521 DOI: 10.1016/j.bpj.2025.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 02/02/2025] [Accepted: 03/17/2025] [Indexed: 03/24/2025] Open
Abstract
Measurements of cell size dynamics have revealed phenomenological principles by which individual cells control their size across diverse organisms. One of the emerging paradigms of cell size homeostasis is the adder, where the cell cycle duration is established such that the cell size increase from birth to division is independent of the newborn cell size. We provide a mechanistic formulation of the adder, considering that cell size follows any arbitrary nonexponential growth law. Our results show that the main requirement to obtain an adder regardless of the growth law (the time derivative of cell size) is that cell cycle regulators are produced at a rate proportional to the growth law, and cell division is triggered when these molecules reach a prescribed threshold level. Among the implications of this generalized adder, we investigate fluctuations in the proliferation of single-cell-derived colonies. Considering exponential cell size growth, random fluctuations in clonal size show a transient increase and then eventually decay to zero over time (i.e., clonal populations become asymptotically more similar). In contrast, several forms of nonexponential cell size dynamics (with adder-based cell size control) yield qualitatively different results: clonal size fluctuations monotonically increase over time, reaching a nonzero value. These results characterize the interplay between cell size homeostasis at the single-cell level and clonal proliferation at the population level, explaining the broad fluctuations in clonal sizes seen in barcoded human cell lines.
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Affiliation(s)
- César Nieto
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware
| | | | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware; Department of Electrical and Computer Engineering, Biomedical Engineering, Mathematical Sciences, Interdisciplinary Neuroscience Program, University of Delaware, Newark, Delaware.
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6
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Olayé J, Bouzidi H, Aristov A, Barizien A, Gutiérrez Ramos S, Baroud C, Bansaye V. Estimation of the lifetime distribution from fluctuations in Bellman-Harris processes. J Math Biol 2025; 90:56. [PMID: 40327121 DOI: 10.1007/s00285-025-02219-8] [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: 04/15/2024] [Revised: 03/31/2025] [Accepted: 04/06/2025] [Indexed: 05/07/2025]
Abstract
The growth of populations without interactions can often be modeled by branching processes where each individual evolves independently and with the same law. In Bellman-Harris processes, each individual lives a random time and is then replaced by a random number of offspring. We are interested in the estimation of the parameters of this model. Our motivation comes from the estimation of cell division time and we focus on Gamma distribution for lifetime and binary reproduction. The mean of the lifetime is closely related to the growth rate of the population. Going farther and describing lifetime variability from fixed time observations is a challenging task, due to the complexity of the fluctuations of non-Markovian branching processes. Using fine results on these fluctuations, we describe two time-asymptotic regimes and explain how to discriminate between them and estimate the parameters. Then, we consider simulations and biological data to validate and discuss our method. It allows to determine single-cell parameters from time-resolved measurements of populations without the need to track each individual or to know the details of the initial condition. The results can be extended to more general branching processes.
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Affiliation(s)
- Jules Olayé
- CMAP, INRIA, École Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France.
| | - Hala Bouzidi
- ENSTA Paris, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Andrey Aristov
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, 75015, Paris, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Antoine Barizien
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, 75015, Paris, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Salomé Gutiérrez Ramos
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, 75015, Paris, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Charles Baroud
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, 75015, Paris, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Vincent Bansaye
- CMAP, INRIA, École Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
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7
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O’Connor OM, Dunlop MJ. Cell-TRACTR: A transformer-based model for end-to-end segmentation and tracking of cells. PLoS Comput Biol 2025; 21:e1013071. [PMID: 40408631 PMCID: PMC12101859 DOI: 10.1371/journal.pcbi.1013071] [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: 07/11/2024] [Accepted: 04/21/2025] [Indexed: 05/25/2025] Open
Abstract
Deep learning-based methods for identifying and tracking cells within microscopy images have revolutionized the speed and throughput of data analysis. These methods for analyzing biological and medical data have capitalized on advances from the broader computer vision field. However, cell tracking can present unique challenges, with frequent cell division events and the need to track many objects with similar visual appearances complicating analysis. Existing architectures developed for cell tracking based on convolutional neural networks (CNNs) have tended to fall short in managing the spatial and global contextual dependencies that are crucial for tracking cells. To overcome these limitations, we introduce Cell-TRACTR (Transformer with Attention for Cell Tracking and Recognition), a novel deep learning model that uses a transformer-based architecture. Cell-TRACTR operates in an end-to-end manner, simultaneously segmenting and tracking cells without the need for post-processing. Alongside this model, we introduce the Cell-HOTA metric, an extension of the Higher Order Tracking Accuracy (HOTA) metric that we adapted to assess cell division. Cell-HOTA differs from standard cell tracking metrics by offering a balanced and easily interpretable assessment of detection, association, and division accuracy. We test our Cell-TRACTR model on datasets of bacteria growing within a defined microfluidic geometry and mammalian cells growing freely in two dimensions. Our results demonstrate that Cell-TRACTR exhibits strong performance in tracking and division accuracy compared to state-of-the-art algorithms, while also meeting traditional benchmarks in detection accuracy. This work establishes a new framework for employing transformer-based models in cell segmentation and tracking.
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Affiliation(s)
- Owen M. O’Connor
- Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Biological Design Center, Boston University, Boston, Massachusetts, United States of America
| | - Mary J. Dunlop
- Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Biological Design Center, Boston University, Boston, Massachusetts, United States of America
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8
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Quinn LK, Sharma K, Faber KT, Orphan VJ. Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground. PNAS NEXUS 2025; 4:pgaf118. [PMID: 40352645 PMCID: PMC12063488 DOI: 10.1093/pnasnexus/pgaf118] [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: 10/05/2024] [Accepted: 03/31/2025] [Indexed: 05/14/2025]
Abstract
Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here, we generated microbially compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex 3D structure of sediments and rocks by adapting a suspension-based, freeze-casting technique commonly used in materials science. Fine-tuning of parameters, such as freezing rate and choice of solvent, provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization (FISH) to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and 13C enrichment in microorganisms, highlighting the potential to directly couple D2O or 13C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant using epifluorescence microscopy. The tool presented here enables highly resolved, spatially explicit, and multimodal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.
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Affiliation(s)
- Laura K Quinn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kriti Sharma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Katherine T Faber
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Victoria J Orphan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
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9
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Schiraldi A. Short- and Long-Term Evolution of Microbial Cultures: A Thermodynamic Perspective. Int J Mol Sci 2025; 26:4187. [PMID: 40362424 PMCID: PMC12071856 DOI: 10.3390/ijms26094187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2025] [Revised: 04/21/2025] [Accepted: 04/25/2025] [Indexed: 05/15/2025] Open
Abstract
A thermodynamic description of cell duplication reflects Odum's view of a feedback energy loop that sustains the transformation of the energy of substrates in the (higher quality) energy of new microbial cells with the dissipation of heat and the (lower quality) energy of catabolites. For a closed batch microbial culture, entropy increases during the whole growth and decay cycle, i.e., the production of entropy during the growth phase displays a rate proportional to the number of cell duplications per unit time, while during the decay phase, it depends on the death rate. Because of its high mobility, water is assumed to exhibit the same thermodynamic activity throughout the system. This assumption leads to the conclusion that an osmotic balance exists between cells and their surrounding medium, which, in a closed batch culture, can affect the rate and the extent of the microbial growth. Finally, the paper suggests a thermodynamic interpretation of the increase in fitness observed in a long-term evolution experiment (LTEE), based on the supposed exergy difference between the generating and generated cells in each duplication, which is also a measure of the "age" of the cells, i.e., aged cells die first. This produces microbial cultures richer in cells with enhanced duplication potential after the many thousand generations considered in an LTEE.
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Affiliation(s)
- Alberto Schiraldi
- Formerly at Department of Food Environment and Nutrition Sciences (DeFENS), University of Milan, 20133 Milan, Italy
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10
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Eremina A, Schwall C, Saez T, Witting L, Kohlheyer D, Martins BMC, Thomas P, Locke JCW. Environmental and molecular noise buffering by the cyanobacterial clock in individual cells. Nat Commun 2025; 16:3566. [PMID: 40234415 PMCID: PMC12000584 DOI: 10.1038/s41467-025-58169-8] [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: 01/24/2024] [Accepted: 03/11/2025] [Indexed: 04/17/2025] Open
Abstract
Circadian clocks enable organisms to anticipate daily cycles, while being robust to molecular and environmental noise. Here, we show how the clock of the cyanobacterium Synechococcus elongatus PCC 7942 buffers genetic and environmental perturbations through its core KaiABC phosphorylation loop. We first characterise single-cell clock dynamics in clock mutants using a microfluidics device that allows precise control of the microenvironment. We find that known clock regulators are dispensable for clock robustness, whilst perturbations of the core clock reveal that the wild type operates at a noise optimum that we can reproduce in a stochastic model of just the core phosphorylation loop. We then examine how the clock responds to noisy environments, including natural light conditions. The model accurately predicts how the clock filters out environmental noise, including fast light fluctuations, to keep time while remaining responsive to environmental shifts. Our findings illustrate how a simple clock network can exhibit complex noise filtering properties, advancing our understanding of how biological circuits can perform accurately in natural environments.
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Affiliation(s)
| | | | - Teresa Saez
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Lennart Witting
- IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | | | | | | | - James C W Locke
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
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11
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Cylke A, Banerjee S. Mechanistic basis for non-exponential bacterial growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.29.646116. [PMID: 40236093 PMCID: PMC11996336 DOI: 10.1101/2025.03.29.646116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Bacterial populations typically exhibit exponential growth under resource-rich conditions, yet individual cells often deviate from this pattern. Recent work has shown that the elongation rates of Escherichia coli and Caulobacter crescentus increase throughout the cell cycle (super-exponential growth), while Bacillus subtilis displays a mid-cycle minimum (convex growth), and Mycobacterium tuberculosis grows linearly. Here, we develop a single-cell model linking gene expression, proteome allocation, and mass growth to explain these diverse growth trajectories. By calibrating model parameters with experimental data, we show that DNA-proportional mRNA transcription produces near-exponential growth, whereas deviations from this proportionality yield the observed non-exponential growth patterns. Analysis of gene expression perturbations reveals that ribosome expression primarily controls dry mass growth rate, whereas envelope expression more strongly affects cell elongation rate. Fitting our model to single-cell experimental data reproduces convex, super-exponential, and linear modes of growth, demonstrating how envelope and ribosome expression schedules drive cell-cycle-specific behaviors. These findings provide a mechanistic basis for non-exponential single-cell growth and offer insights into how bacterial cells dynamically regulate elongation rates within each generation.
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12
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Proenca AM, Rang CU, Chao L. A link between aging and persistence. Antimicrob Agents Chemother 2025; 69:e0131324. [PMID: 39982072 PMCID: PMC11963536 DOI: 10.1128/aac.01313-24] [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: 08/31/2024] [Accepted: 01/28/2025] [Indexed: 02/22/2025] Open
Abstract
Despite the various strategies that microorganisms have evolved to resist antibiotics, survival to drug treatments can be driven by subpopulations of susceptible bacteria in a transient state of dormancy. This phenotype, known as bacterial persistence, arises due to a natural and ubiquitous heterogeneity of growth states in bacterial populations. Nonetheless, the unifying mechanism of persistence remains unknown, with several pathways being able to trigger the phenotype. Here, we show that asymmetric damage partitioning, a form of cellular aging, produces the underlying phenotypic heterogeneity upon which persistence is triggered. Using single-cell microscopy and microfluidic devices, we demonstrate that deterministic asymmetry in exponential phase populations leads to a state of growth stability, which prevents the spontaneous formation of persisters. However, as populations approach stationary phase, aging bacteria-those inheriting more damage upon division-exhibit a sharper growth rate decline, increased probability of growth arrest, and higher persistence rates. These results indicate that persistence triggers are biased by bacterial asymmetry, thus acting upon the deterministic heterogeneity produced by cellular aging. This work suggests unifying mechanisms for persistence and offers new perspectives on the treatment of recalcitrant infections.
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Affiliation(s)
- A. M. Proenca
- Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - C. U. Rang
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - L. Chao
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
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13
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Espinoza Miranda SS, Abbaszade G, Hess WR, Drescher K, Saliba AE, Zaburdaev V, Chai L, Dreisewerd K, Grünberger A, Westendorf C, Müller S, Mascher T. Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges. Microbiol Mol Biol Rev 2025; 89:e0013824. [PMID: 39853129 PMCID: PMC11948493 DOI: 10.1128/mmbr.00138-24] [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] [Indexed: 01/26/2025] Open
Abstract
SUMMARYThe development of multicellularity represents a key evolutionary transition that is crucial for the emergence of complex life forms. Although multicellularity has traditionally been studied in eukaryotes, it originates in prokaryotes. Coordinated aggregation of individual cells within the confines of a colony results in emerging, higher-level functions that benefit the population as a whole. During colony differentiation, an almost infinite number of ecological and physiological population-forming forces are at work, creating complex, intricate colony structures with divergent functions. Understanding the assembly and dynamics of such populations requires resolving individual cells or cell groups within such macroscopic structures. Addressing how each cell contributes to the collective action requires pushing the resolution boundaries of key technologies that will be presented in this review. In particular, single-cell techniques provide powerful tools for studying bacterial multicellularity with unprecedented spatial and temporal resolution. These advancements include novel microscopic techniques, mass spectrometry imaging, flow cytometry, spatial transcriptomics, single-bacteria RNA sequencing, and the integration of spatiotemporal transcriptomics with microscopy, alongside advanced microfluidic cultivation systems. This review encourages exploring the synergistic potential of the new technologies in the study of bacterial multicellularity, with a particular focus on individuals in differentiated bacterial biofilms (colonies). It highlights how resolving population structures at the single-cell level and understanding their respective functions can elucidate the overarching functions of bacterial multicellular populations.
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Affiliation(s)
| | | | - Wolfgang R. Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | | | - Antoine-Emmanuel Saliba
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Vasily Zaburdaev
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Liraz Chai
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Alexander Grünberger
- Microsystems in Bioprocess Engineering (μBVT), Institute of Process Engineering in Life Sciences (BLT), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Christian Westendorf
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Leipzig, Germany
| | - Susann Müller
- Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Thorsten Mascher
- General Microbiology, Technische Universität Dresden, Dresden, Germany
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14
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Joesaar A, Holub M, Lutze L, Emanuele M, Kerssemakers J, Pabst M, Dekker C. A microfluidic platform for extraction and analysis of bacterial genomic DNA. LAB ON A CHIP 2025; 25:1767-1775. [PMID: 40026014 PMCID: PMC11873781 DOI: 10.1039/d4lc00839a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Accepted: 02/23/2025] [Indexed: 03/04/2025]
Abstract
Bacterial cells organize their genomes into a compact hierarchical structure called the nucleoid. Studying the nucleoid in cells faces challenges because of the cellular complexity while in vitro assays have difficulty in handling the fragile megabase-scale DNA biopolymers that make up bacterial genomes. Here, we introduce a method that overcomes these limitations as we develop and use a microfluidic device for the sequential extraction, purification, and analysis of bacterial nucleoids in individual microchambers. Our approach avoids any transfer or pipetting of the fragile megabase-size genomes and thereby prevents their fragmentation. We show how the microfluidic system can be used to extract and analyze single chromosomes from B. subtilis cells. Upon on-chip lysis, the bacterial genome expands in size and DNA-binding proteins are flushed away. Subsequently, exogeneous proteins can be added to the trapped DNA via diffusion. We envision that integrated microfluidic platforms will become an essential tool for the bottom-up assembly of complex biomolecular systems such as artificial chromosomes.
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Affiliation(s)
- Alex Joesaar
- Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Martin Holub
- Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Leander Lutze
- Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Marco Emanuele
- Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Jacob Kerssemakers
- Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Martin Pabst
- Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Cees Dekker
- Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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15
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Hobson-Gutierrez S, Kussell E. Evolutionary Advantage of Cell Size Control. PHYSICAL REVIEW LETTERS 2025; 134:118401. [PMID: 40192351 DOI: 10.1103/physrevlett.134.118401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 01/24/2025] [Indexed: 04/25/2025]
Abstract
We analyze the advantage of cell size control strategies in growing populations under mortality constraints and show that growth-dependent mortality can select for accurate size control. We determine how mortality, noise, and nongenetic heritability of cell size impact long-term population growth. We derive an analytical expression for the optimal cell size. We demonstrate that size heritability enables selection to act on the distribution of cell sizes in a population to avoid viability thresholds and adapt to size- and growth-dependent mortality landscapes.
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Affiliation(s)
| | - Edo Kussell
- New York University, Department of Biology, 12 Waverly Place, New York, New York 10003, USA
- New York University, Department of Physics, 726 Broadway, New York, New York 10003, USA
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16
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Papagiannakis A, Yu Q, Govers SK, Lin WH, Wingreen NS, Jacobs-Wagner C. Nonequilibrium polysome dynamics promote chromosome segregation and its coupling to cell growth in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.10.08.617237. [PMID: 40161845 PMCID: PMC11952301 DOI: 10.1101/2024.10.08.617237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Chromosome segregation is essential for cellular proliferation. Unlike eukaryotes, bacteria lack cytoskeleton-based machinery to segregate their chromosomal DNA (nucleoid). The bacterial ParABS system segregates the duplicated chromosomal regions near the origin of replication. However, this function does not explain how bacterial cells partition the rest (bulk) of the chromosomal material. Furthermore, some bacteria, including Escherichia coli, lack a ParABS system. Yet, E. coli faithfully segregates nucleoids across various growth rates. Here, we provide theoretical and experimental evidence that polysome production during chromosomal gene expression helps compact, split, segregate, and position nucleoids in E. coli through out-of-equilibrium dynamics and polysome exclusion from the DNA meshwork, inherently coupling these processes to biomass growth across nutritional conditions. Halting chromosomal gene expression and thus polysome production immediately stops sister nucleoid migration while ensuing polysome depletion gradually reverses nucleoid segregation. Redirecting gene expression away from the chromosome and toward plasmids causes ectopic polysome accumulations that are sufficient to drive aberrant nucleoid dynamics. Cell width enlargement suggest that the proximity of the DNA to the membrane along the radial axis is important to limit the exchange of polysomes across DNA-free regions, ensuring nucleoid segregation along the cell length. Our findings suggest a self-organizing mechanism for coupling nucleoid segregation to cell growth.
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Affiliation(s)
- Alexandros Papagiannakis
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Qiwei Yu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton NJ 08544, USA
| | - Sander K Govers
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Wei-Hsiang Lin
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA 94305, USA
| | - Ned S Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton NJ 08544, USA
| | - Christine Jacobs-Wagner
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford, CA 94305, USA
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17
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Mobaraki M, Deng C, Zheng J, Li H. Yeast aging from a dynamic systems perspective: Analysis of single cell trajectories reveals significant interplay between nuclear size scaling, proteasome dynamics, and mitochondrial morphology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.11.642143. [PMID: 40161634 PMCID: PMC11952390 DOI: 10.1101/2025.03.11.642143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Yeast replicative aging is cell autonomous and thus a good model for mechanistic study from a dynamic systems perspective. Utilizing an engineered strain of yeast with a switchable genetic program to arrest daughter cells (without affecting mother cell divisions) and a high throughput microfluidic device, we systematically analyze the dynamic trajectories of thousands of single yeast mother cells throughout their lifespan, using fluorescent reporters that cover a range of biological processes, including some major aging hallmarks. We found that the markers of proteostasis stand out as most predictive of the lifespan of individual cells. In particular, nuclear proteasome concentration at middle age is a good predictor. We found that cell size (measured by area) grows linearly with time, and that nuclear size grows in proportion to maintain isometric scaling in young cells. As the cells become older, their nuclear size increases faster than linear and isometric size scaling breaks down. We observed that proteasome concentration in the nucleus exhibits dynamics very different from that in cytoplasm, with much more rapid decrease during aging; such dynamic behavior can be accounted for by the change of nuclear size in a simple mathematical model of transport. We hypothesize that the gradual increase of cell size and the associated nuclear size increase lead to the dilution of important nuclear factors (such as proteasome) that drives aging. We also show that perturbing proteasome changes mitochondria morphology and function, but not vice versa, potentially placing the change of proteosome upstream of the change of mitochondrial phenotypes. Our study produced large scale single cell dynamic data that can serve as a valuable resource for the aging research community to analyze the dynamics of other markers and potential causal relations between them. It is also a useful resource for building and testing physics/AI based models that identify early dynamics events predictive of lifespan and can be targets for longevity interventions.
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Affiliation(s)
- Michael Mobaraki
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Developmental Stem Cell Biology Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Changhui Deng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jiashun Zheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
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18
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Kumar S, Inns PG, Ward S, Lagage V, Wang J, Kaminska R, Booth MJ, Uphoff S, Cohen EAK, Mamou G, Kleanthous C. Immobile lipopolysaccharides and outer membrane proteins differentially segregate in growing Escherichia coli. Proc Natl Acad Sci U S A 2025; 122:e2414725122. [PMID: 40030021 PMCID: PMC11912417 DOI: 10.1073/pnas.2414725122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 01/07/2025] [Indexed: 03/19/2025] Open
Abstract
The outer membrane (OM) of gram-negative bacteria is a robust, impermeable barrier that excludes many classes of antibiotics. Contrary to the classical model of an asymmetric lipid bilayer, recent evidence suggests the OM is predominantly an asymmetric proteolipid membrane (APLM). Outer leaflet lipopolysaccharides (LPS) that surround integral β-barrel outer membrane proteins (OMPs) are shared with other OMPs to form a supramolecular network in which the levels of OMPs approach those of LPS. Some of the most abundant OMPs in the Escherichia coli OM are trimeric porins. How porins and LPS are incorporated into the OM of growing bacteria is poorly understood. Here, we use live-cell imaging and microfluidics to investigate how LPS, labeled using click chemistry, and the porin OmpF, labeled using the bacteriocin colicin N, are incorporated into the E. coli OM. Diffraction-limited fluorescence microscopy shows OmpF and LPS to be uniformly distributed and immobile. However, clustering of both macromolecules becomes evident by superresolution microscopy, which is also the case for their biogenesis proteins, BamA and LptD, respectively. Notwithstanding these common organizational features, OmpF insertion into the OM is cell-cycle-dependent leading to binary partitioning and strong polar accumulation of old OmpF. Old LPS on the other hand is diluted ~50% at each division cycle by new LPS, resulting in only mild polar accumulation of preexisting LPS. We conclude that although LPS and OMPs are destined to form the APLM their insertion dynamics are fundamentally different, which has major implications for understanding how the OM is assembled.
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Affiliation(s)
- Sandip Kumar
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Patrick G. Inns
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Scott Ward
- Department of Mathematics, Imperial College London, LondonSW7 1AZ, United Kingdom
| | - Valentine Lagage
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Jingyu Wang
- Department of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Martin J. Booth
- Department of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Edward A. K. Cohen
- Department of Mathematics, Imperial College London, LondonSW7 1AZ, United Kingdom
| | - Gideon Mamou
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
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19
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Genthon A. From noisy cell size control to population growth: When variability can be beneficial. Phys Rev E 2025; 111:034407. [PMID: 40247490 DOI: 10.1103/physreve.111.034407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Accepted: 02/19/2025] [Indexed: 04/19/2025]
Abstract
Single-cell experiments revealed substantial variability in generation times, growth rates, but also in birth and division sizes between genetically identical cells. Understanding how these fluctuations determine the fitness of the population, i.e., its growth rate, is necessary in any quantitative theory of evolution. Here, we develop a biologically relevant model which accounts for the stochasticity in single-cell growth rates, birth sizes, and division sizes. We derive expressions for the population growth rate and mean birth size in the population in terms of single-cell fluctuations. Allowing division sizes to fluctuate reveals how the mechanism of cell size control (timer, sizer, and adder) influences population growth. Surprisingly, we find that fluctuations in single-cell growth rates can be beneficial for population growth when slow-growing cells tend to divide at smaller sizes than fast-growing cells. Our framework is not limited to exponentially growing cells like Escherichia coli, and we derive similar expressions for cells with linear and bilinear growth laws, such as Mycobacterium tuberculosis and fission yeast Schizosaccharomyces pombe, respectively.
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Affiliation(s)
- Arthur Genthon
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
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20
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Rossine F, Sanchez C, Eaton D, Paulsson J, Baym M. Intracellular competition shapes plasmid population dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.19.639193. [PMID: 40027608 PMCID: PMC11870584 DOI: 10.1101/2025.02.19.639193] [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: 03/05/2025]
Abstract
Conflicts between levels of biological organization are central to evolution, from populations of multicellular organisms to selfish genetic elements in microbes. Plasmids are extrachromosomal, self-replicating genetic elements that underlie much of the evolutionary flexibility of bacteria. Evolving plasmids face selective pressures on their hosts, but also compete within the cell for replication, making them an ideal system for studying the joint dynamics of multilevel selection. While theory indicates that within-cell selection should matter for plasmid evolution, experimental measurement of within-cell plasmid fitness and its consequences has remained elusive. Here we measure the within-cell fitness of competing plasmids and characterize drift and selective dynamics. We achieve this by the controlled splitting of synthetic plasmid dimers to create balanced competition experiments. We find that incompatible plasmids co-occur for longer than expected due to methylation-based plasmid eclipsing. During this period of co-occurrence, less transcriptionally active plasmids display a within-cell selective advantage over their competing plasmids, leading to preferential fixation of silent plasmids. When the transcribed gene is beneficial to the cell, for example an antibiotic resistance gene, there is a cell-plasmid fitness tradeoff mediated by the dominance of the beneficial trait. Surprisingly, more dominant plasmid-encoded traits are less likely to fix but more likely to initially invade than less dominant traits. Taken together, our results show that plasmid evolution is driven by dynamics at two levels, with a transient, but critical, contribution of within-cell fitness.
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Affiliation(s)
- Fernando Rossine
- Departments of Biomedical Informatics and Microbiology, and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Carlos Sanchez
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Daniel Eaton
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Johan Paulsson
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Michael Baym
- Departments of Biomedical Informatics and Microbiology, and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
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21
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Teo AJT, Gu J, Govyadinov A, Kornilovitch P, Wang P, Goh S, Tung NT, Peng Z, Koh K, Li KHH. Development of a Mass-Producible Microfluidic Device for Single and Bulk Mycobacteria Investigations. BIOSENSORS 2025; 15:108. [PMID: 39997010 PMCID: PMC11853077 DOI: 10.3390/bios15020108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2024] [Revised: 01/23/2025] [Accepted: 01/27/2025] [Indexed: 02/26/2025]
Abstract
We developed a mass-producible microfluidic device capable of long-term observations of single bacilli and bulk bacteria culture interactions for subsequent antimicrobial resistance (AMR) studies. The device provides high consistency across separate devices due to its standardized manufacturing process unlike conventional microfluidic devices. Mycobacteria bovis BCG and M. smegmatis are trapped within the microfluidic device using minimal equipment and capillary-based techniques, acting as a surrogate model for the highly pathogenic bacteria M. tuberculosis. Individual bacilli and bulk bacteria aggregates were observed across a span of ten growth cycles, revealing bacteria growth morphologies alike those in past research. We accordingly propose that this chip would be appropriate for observations of AMR trials involving M. tuberculosis.
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Affiliation(s)
- Adrian J. T. Teo
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Singapore; (A.J.T.T.); (K.K.)
| | - Jianhui Gu
- HP Singapore Pte Ltd., 1A Depot Close, Singapore 109842, Singapore; (J.G.); (P.W.); (S.G.)
| | | | - Pavel Kornilovitch
- HP Pte Ltd., Corvallis, OR 97330, USA; (A.G.); (P.K.)
- Department of Physics, Oregon State University, Corvallis, OR 97331, USA
| | - Peiyun Wang
- HP Singapore Pte Ltd., 1A Depot Close, Singapore 109842, Singapore; (J.G.); (P.W.); (S.G.)
| | - Serene Goh
- HP Singapore Pte Ltd., 1A Depot Close, Singapore 109842, Singapore; (J.G.); (P.W.); (S.G.)
| | - Nguyen Truong Tung
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 639798, Singapore;
| | - Zhen Peng
- School of Mechanical Engineering, State Key Laboratory of Intelligent Construction and Healthy Operation and Maintenance of Deep Underground Engineering, Sichuan University, Chengdu 610065, China;
| | - Keith Koh
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Singapore; (A.J.T.T.); (K.K.)
| | - King Ho Holden Li
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Singapore; (A.J.T.T.); (K.K.)
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22
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Pavlou A, Cinquemani E, Pinel C, Giordano N, Mathilde VMG, Mihalcescu I, Geiselmann J, de Jong H. Single-cell data reveal heterogeneity of investment in ribosomes across a bacterial population. Nat Commun 2025; 16:285. [PMID: 39746998 PMCID: PMC11695989 DOI: 10.1038/s41467-024-55394-5] [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: 04/10/2024] [Accepted: 12/10/2024] [Indexed: 01/04/2025] Open
Abstract
Ribosomes are responsible for the synthesis of proteins, the major component of cellular biomass. Classical experiments have established a linear relationship between the fraction of resources invested in ribosomal proteins and the rate of balanced growth of a microbial population. Very little is known, however, about how the investment in ribosomes varies over individual cells in a population. We therefore extended the study of ribosomal resource allocation from populations to single cells, using a combination of time-lapse fluorescence microscopy and statistical inference. We found a large variability of ribosome concentrations and growth rates in conditions of balanced growth of the model bacterium Escherichia coli in a given medium, which cannot be accounted for by the population-level growth law. A large variability in the allocation of resources to ribosomes was also found during the transition of the bacteria from a poor to a rich growth medium. While some cells immediately adapt their ribosome synthesis rate to the new environment, others do so only gradually. Our results thus reveal a range of strategies for investing resources in the molecular machines at the heart of cellular self-replication. This raises the fundamental question whether the observed variability is an intrinsic consequence of the stochastic nature of the underlying biochemical processes or whether it improves the fitness of Escherichia coli in its natural environment.
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Affiliation(s)
- Antrea Pavlou
- Univ. Grenoble Alpes, Inria, Grenoble, France
- Univ. Grenoble Alpes, CNRS, LIPhy, Grenoble, France
| | - Eugenio Cinquemani
- Univ. Grenoble Alpes, Inria, Grenoble, France
- Univ. Grenoble Alpes, CNRS, LIPhy, Grenoble, France
| | - Corinne Pinel
- Univ. Grenoble Alpes, Inria, Grenoble, France
- Univ. Grenoble Alpes, CNRS, LIPhy, Grenoble, France
| | - Nils Giordano
- Nantes Université, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | | | | | - Johannes Geiselmann
- Univ. Grenoble Alpes, Inria, Grenoble, France.
- Univ. Grenoble Alpes, CNRS, LIPhy, Grenoble, France.
| | - Hidde de Jong
- Univ. Grenoble Alpes, Inria, Grenoble, France.
- Univ. Grenoble Alpes, CNRS, LIPhy, Grenoble, France.
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23
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Chong SW, Shen Y, Palomba S, Vigolo D. Nanofluidic Lab-On-A-Chip Systems for Biosensing in Healthcare. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2025; 21:e2407478. [PMID: 39491535 DOI: 10.1002/smll.202407478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Revised: 10/21/2024] [Indexed: 11/05/2024]
Abstract
Biosensing plays a vital role in healthcare monitoring, disease detection, and treatment planning. In recent years, nanofluidic technology has been increasingly explored to be developed into lab-on-a-chip biosensing systems. Given now the possibility of fabricating geometrically defined nanometric channels that are commensurate with the size of many biomolecules, nanofluidic-based devices are likely to become a key technology for the analysis of various clinical biomarkers, including DNA (deoxyribonucleic acid) and proteins in liquid biopsies. This review summarizes the fundamentals and technological advances of nanofluidics from the purview of single-molecule analysis, detection of low-abundance molecules, and single-cell analysis at the subcellular level. The extreme confinement and dominant surface charge effects in nanochannels provide unique advantages to nanofluidic devices for the manipulation and transport of target biomarkers. When coupled to a microfluidic network to facilitate sample introduction, integrated micro-nanofluidic biosensing devices are proving to be more sensitive and specific in molecular analysis compared to conventional assays in many cases. Based on recent progress in nanofluidics and current clinical trends, the review concludes with a discussion of near-term challenges and future directions for the development of nanofluidic-based biosensing systems toward enabling a new wave of lab-on-a-chip technology for personalized and preventive medicine.
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Affiliation(s)
- Shin Wei Chong
- School of Biomedical Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Yi Shen
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Stefano Palomba
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Physics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Daniele Vigolo
- School of Biomedical Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
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24
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Golchin A, Shams F, Moradi F, Sadrabadi AE, Parviz S, Alipour S, Ranjbarvan P, Hemmati Y, Rahnama M, Rasmi Y, Aziz SGG. Single-cell Technology in Stem Cell Research. Curr Stem Cell Res Ther 2025; 20:9-32. [PMID: 38243989 DOI: 10.2174/011574888x265479231127065541] [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: 07/11/2023] [Revised: 09/23/2023] [Accepted: 10/04/2023] [Indexed: 01/22/2024]
Abstract
Single-cell technology (SCT), which enables the examination of the fundamental units comprising biological organs, tissues, and cells, has emerged as a powerful tool, particularly in the field of biology, with a profound impact on stem cell research. This innovative technology opens new pathways for acquiring cell-specific data and gaining insights into the molecular pathways governing organ function and biology. SCT is not only frequently used to explore rare and diverse cell types, including stem cells, but it also unveils the intricacies of cellular diversity and dynamics. This perspective, crucial for advancing stem cell research, facilitates non-invasive analyses of molecular dynamics and cellular functions over time. Despite numerous investigations into potential stem cell therapies for genetic disorders, degenerative conditions, and severe injuries, the number of approved stem cell-based treatments remains limited. This limitation is attributed to the various heterogeneities present among stem cell sources, hindering their widespread clinical utilization. Furthermore, stem cell research is intimately connected with cutting-edge technologies, such as microfluidic organoids, CRISPR technology, and cell/tissue engineering. Each strategy developed to overcome the constraints of stem cell research has the potential to significantly impact advanced stem cell therapies. Drawing on the advantages and progress achieved through SCT-based approaches, this study aims to provide an overview of the advancements and concepts associated with the utilization of SCT in stem cell research and its related fields.
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Affiliation(s)
- Ali Golchin
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
- Department of Clinical Biochemistry and Applied Cell Sciences, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Forough Shams
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid, Beheshti University of Medical Sciences, Tehran, Iran
| | - Faezeh Moradi
- Department of Tissue Engineering, School of Medicine, Tarbiat Modares University, Tehran, Iran
| | - Amin Ebrahimi Sadrabadi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran
| | - Shima Parviz
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz, University of Medical Sciences, Shiraz, Iran
| | - Shahriar Alipour
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
- Department of Clinical Biochemistry and Applied Cell Sciences, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Parviz Ranjbarvan
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
- Department of Clinical Biochemistry and Applied Cell Sciences, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Yaser Hemmati
- Department of Prosthodontics, Dental Faculty, Urmia University of Medical Science, Urmia, Iran
| | - Maryam Rahnama
- Department of Clinical Biochemistry and Applied Cell Sciences, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Yousef Rasmi
- Department of Clinical Biochemistry and Applied Cell Sciences, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Shiva Gholizadeh-Ghaleh Aziz
- Department of Clinical Biochemistry and Applied Cell Sciences, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
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25
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Nakaoka H. Live Imaging of Fission Yeast Single-Cell Lineages Using a Microfluidic Device. Methods Mol Biol 2025; 2862:61-76. [PMID: 39527193 DOI: 10.1007/978-1-0716-4168-2_5] [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] [Indexed: 11/16/2024]
Abstract
Mother machine (MM) is a microfluidic device originally developed for long-term live imaging of Escherichia coli bacterial cells under a microscope. The simple yet sophisticated design has enabled microbiologists to track multiple single-cell lineages cultured under highly controlled external environments. Here, I describe how to fabricate a fission yeast version of MM with photolithography and soft lithography. Procedures for setting up the microfluidic device for long-term live microscopy are also explained.
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Affiliation(s)
- Hidenori Nakaoka
- Department of Optical Imaging, Advanced Research Promotion Center, Tokushima University, Tokushima, Japan.
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26
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Sahm A, Riege K, Groth M, Bens M, Kraus J, Fischer M, Kestler H, Englert C, Schaible R, Platzer M, Hoffmann S. Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype. Genome Res 2024; 34:2217-2228. [PMID: 39632086 PMCID: PMC11694757 DOI: 10.1101/gr.279025.124] [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: 01/23/2024] [Accepted: 10/18/2024] [Indexed: 12/07/2024]
Abstract
Growing evidence suggests that somatic mutations may be a major cause of the aging process. However, it remains to be tested whether the predictions of the theory also apply to species with longer life spans than humans. Hydra is a genus of freshwater polyps with remarkable regeneration abilities and a potentially unlimited life span under laboratory conditions. By genome sequencing of single cells and whole animals, we found that the mutation rates in Hydra's stem cells are even slightly higher than in humans or mice. A potential explanation for this deviation from the prediction of the theory may lie in the adaptability offered by a higher mutation rate, as we were able to show that the genome of the widely studied Hydra magnipapillata strain 105 has undergone a process of strong positive selection since the strain's cultivation 50 years ago. This most likely represents a rapid adaptation to the drastically altered environmental conditions associated with the transition from the wild to laboratory conditions. Processes under positive selection in captive animals include pathways associated with Hydra's simple nervous system, its nucleic acid metabolic process, cell migration, and hydrolase activity.
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Affiliation(s)
- Arne Sahm
- Computational Phenomics group, IUF-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany;
- Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
- Computational Phenomics group, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Marco Groth
- Core Facility Next Generation Sequencing, Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Martin Bens
- Core Facility Next Generation Sequencing, Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Johann Kraus
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Hans Kestler
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Christoph Englert
- Molecular Genetics Lab, Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
- Institute of Biochemistry and Biophysics, Friedrich Schiller University Jena, 07745 Jena, Germany
| | - Ralf Schaible
- Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Matthias Platzer
- Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
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27
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Mäkelä J, Papagiannakis A, Lin WH, Lanz MC, Glenn S, Swaffer M, Marinov GK, Skotheim JM, Jacobs-Wagner C. Genome concentration limits cell growth and modulates proteome composition in Escherichia coli. eLife 2024; 13:RP97465. [PMID: 39714909 DOI: 10.7554/elife.97465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2024] Open
Abstract
Defining the cellular factors that drive growth rate and proteome composition is essential for understanding and manipulating cellular systems. In bacteria, ribosome concentration is known to be a constraining factor of cell growth rate, while gene concentration is usually assumed not to be limiting. Here, using single-molecule tracking, quantitative single-cell microscopy, and modeling, we show that genome dilution in Escherichia coli cells arrested for DNA replication limits total RNA polymerase activity within physiological cell sizes across tested nutrient conditions. This rapid-onset limitation on bulk transcription results in sub-linear scaling of total active ribosomes with cell size and sub-exponential growth. Such downstream effects on bulk translation and cell growth are near-immediately detectable in a nutrient-rich medium, but delayed in nutrient-poor conditions, presumably due to cellular buffering activities. RNA sequencing and tandem-mass-tag mass spectrometry experiments further reveal that genome dilution remodels the relative abundance of mRNAs and proteins with cell size at a global level. Altogether, our findings indicate that chromosome concentration is a limiting factor of transcription and a global modulator of the transcriptome and proteome composition in E. coli. Experiments in Caulobacter crescentus and comparison with eukaryotic cell studies identify broadly conserved DNA concentration-dependent scaling principles of gene expression.
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Affiliation(s)
- Jarno Mäkelä
- Howard Hughes Medical Institute, Stanford University, Stanford, United States
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, United States
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Alexandros Papagiannakis
- Howard Hughes Medical Institute, Stanford University, Stanford, United States
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, United States
| | - Wei-Hsiang Lin
- Howard Hughes Medical Institute, Stanford University, Stanford, United States
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, United States
| | - Michael Charles Lanz
- Department of Biology, Stanford University, Stanford, United States
- Chan Zuckerberg Biohub, Stanford, United Kingdom
| | - Skye Glenn
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, United States
- Department of Biology, Stanford University, Stanford, United States
| | - Matthew Swaffer
- Department of Biology, Stanford University, Stanford, United States
| | - Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, United States
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, United States
- Chan Zuckerberg Biohub, Stanford, United Kingdom
| | - Christine Jacobs-Wagner
- Howard Hughes Medical Institute, Stanford University, Stanford, United States
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, United States
- Department of Biology, Stanford University, Stanford, United States
- Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, United States
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28
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Sidor LM, Beaulieu MM, Rasskazov I, Acarturk BC, Ren J, Jenen E, Kamoen L, Vitali MV, Carney PS, Schmidt GR, Srubar WV, Abbondanzieri EA, Meyer AS. Engineered bacteria that self-assemble bioglass polysilicate coatings display enhanced light focusing. Proc Natl Acad Sci U S A 2024; 121:e2409335121. [PMID: 39656206 DOI: 10.1073/pnas.2409335121] [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: 05/09/2024] [Accepted: 10/17/2024] [Indexed: 12/18/2024] Open
Abstract
Cutting-edge photonic devices frequently rely on microparticle components to focus and manipulate light. Conventional methods used to produce these microparticle components frequently offer limited control of their structural properties or require low-throughput nanofabrication of more complex structures. Here, we employ a synthetic biology approach to produce environmentally friendly, living microlenses with tunable structural properties. We engineered Escherichia coli bacteria to display the silica biomineralization enzyme silicatein from aquatic sea sponges. Our silicatein-expressing bacteria can self-assemble a shell of polysilicate "bioglass" around themselves. Remarkably, the polysilicate-encapsulated bacteria can focus light into intense nanojets that are nearly an order of magnitude brighter than unmodified bacteria. Polysilicate-encapsulated bacteria are metabolically active for up to 4 mo, potentially allowing them to sense and respond to stimuli over time. Our data demonstrate that synthetic biology offers a pathway for producing inexpensive and durable photonic components that exhibit unique optical properties.
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Affiliation(s)
- Lynn M Sidor
- Department of Biology, University of Rochester, Rochester, NY 14627
| | - Michelle M Beaulieu
- Department of Physics and Astronomy, University of Rochester, Rochester, NY 14627
| | - Ilia Rasskazov
- Institute of Optics, University of Rochester, Rochester, NY 14627
| | - B Cansu Acarturk
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO 80309
| | - Jie Ren
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO 80309
| | - Emerson Jenen
- Department of Biology, University of Rochester, Rochester, NY 14627
| | - Lycka Kamoen
- Department of Biotechnology, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - María Vázquez Vitali
- Department of Biotechnology, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - P Scott Carney
- Institute of Optics, University of Rochester, Rochester, NY 14627
| | - Greg R Schmidt
- Institute of Optics, University of Rochester, Rochester, NY 14627
| | - Wil V Srubar
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO 80309
- Materials Science and Engineering Program, University of Colorado Boulder, Boulder, CO 80309
| | | | - Anne S Meyer
- Department of Biology, University of Rochester, Rochester, NY 14627
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29
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Campey A, Łapińska U, Chait R, Tsaneva-Atanasova K, Pagliara S. Antibiotic resistant bacteria survive treatment by doubling while shrinking. mBio 2024; 15:e0237524. [PMID: 39565111 PMCID: PMC11633386 DOI: 10.1128/mbio.02375-24] [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: 08/02/2024] [Accepted: 10/22/2024] [Indexed: 11/21/2024] Open
Abstract
Many antibiotics that are used in healthcare, farming, and aquaculture end up in environments with different spatial structures that might promote heterogeneity in the emergence of antibiotic resistance. However, the experimental evolution of microbes at sub-inhibitory concentrations of antibiotics has been mainly carried out at the population level which does not allow capturing single-cell responses to antibiotics. Here, we investigate and compare the emergence of resistance to ciprofloxacin in Escherichia coli in well-mixed and structured environments using experimental evolution, genomics, and microfluidics-based time-lapse microscopy. We discover that resistance to ciprofloxacin and cross-resistance to other antibiotics is stronger in the well-mixed environment due to the emergence of target mutations, whereas efflux regulator mutations emerge in the structured environment. The latter mutants also harbor sub-populations of persisters that survive high concentrations of ciprofloxacin that inhibit bacterial growth at the population level. In contrast, genetically resistant bacteria that display target mutations also survive high concentrations of ciprofloxacin that inhibit their growth via population-level antibiotic tolerance. These resistant and tolerant bacteria keep doubling while shrinking in size in the presence of ciprofloxacin and regain their original size after antibiotic removal, which constitutes a newly discovered phenotypic response. This new knowledge sheds light on the diversity of strategies employed by bacteria to survive antibiotics and poses a stepping stone for understanding the link between mutations at the population level and phenotypic single-cell responses. IMPORTANCE The evolution of antimicrobial resistance poses a pressing challenge to global health with an estimated 5 million deaths associated with antimicrobial resistance every year globally. Here, we investigate the diversity of strategies employed by bacteria to survive antibiotics. We discovered that bacteria evolve genetic resistance to antibiotics while simultaneously displaying tolerance to very high doses of antibiotics by doubling while shrinking in size.
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Affiliation(s)
- Adrian Campey
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Remy Chait
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Krasimira Tsaneva-Atanasova
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
- EPSRC Hub for Quantitative Modelling in Healthcare, University of Exeter, Exeter, Devon, United Kingdom
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
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30
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Blassick CM, Lugagne JB, Dunlop MJ. Dynamic heterogeneity in an E. coli stress response regulon mediates gene activation and antimicrobial peptide tolerance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.27.625634. [PMID: 39677761 PMCID: PMC11642793 DOI: 10.1101/2024.11.27.625634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
The bacterial stress response is an intricately regulated system that plays a critical role in cellular resistance to drug treatment. The complexity of this response is further complicated by cell-to-cell heterogeneity in the expression of bacterial stress response genes. These genes are often organized into networks comprising one or more transcriptional regulators that control expression of a suite of downstream genes. While the expression heterogeneity of many of these upstream regulators has been characterized, the way in which this variability affects the larger downstream stress response remains hard to predict, prompting two key questions. First, how does heterogeneity and expression noise in stress response regulators propagate to the diverse downstream genes in their regulons. Second, when expression levels vary, how do multiple downstream genes act together to protect cells from stress. To address these questions, we focus on the transcription factor PhoP, a critical virulence regulator which coordinates pathogenicity in several gram-negative species. We use optogenetic stimulation to precisely control PhoP expression levels and examine how variations in PhoP affect the downstream activation of genes in the PhoP regulon. We find that these downstream genes exhibit differences both in mean expression level and sensitivity to increasing levels of PhoP. These response functions can also vary between individual cells, increasing heterogeneity in the population. We tie these variations to cell survival when bacteria are exposed to a clinically-relevant antimicrobial peptide, showing that high expression of the PhoP-regulon gene pmrD provides a protective effect against Polymyxin B. Overall, we demonstrate that even subtle heterogeneity in expression of a stress response regulator can have clear consequences for enabling bacteria to survive stress.
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31
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Chung ES, Kar P, Kamkaew M, Amir A, Aldridge BB. Single-cell imaging of the Mycobacterium tuberculosis cell cycle reveals linear and heterogenous growth. Nat Microbiol 2024; 9:3332-3344. [PMID: 39548343 PMCID: PMC11602732 DOI: 10.1038/s41564-024-01846-z] [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: 05/18/2023] [Accepted: 10/03/2024] [Indexed: 11/17/2024]
Abstract
Difficulties in antibiotic treatment of Mycobacterium tuberculosis (Mtb) are partly thought to be due to heterogeneity in growth. Although the ability of bacterial pathogens to regulate growth is crucial to control homeostasis, virulence and drug responses, single-cell growth and cell cycle behaviours of Mtb are poorly characterized. Here we use time-lapse, single-cell imaging of Mtb coupled with mathematical modelling to observe asymmetric growth and heterogeneity in cell size, interdivision time and elongation speed. We find that, contrary to Mycobacterium smegmatis, Mtb initiates cell growth not only from the old pole but also from new poles or both poles. Whereas most organisms grow exponentially at the single-cell level, Mtb has a linear growth mode. Our data show that the growth behaviour of Mtb diverges from that of model bacteria, provide details into how Mtb grows and creates heterogeneity and suggest that growth regulation may also diverge from that in other bacteria.
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Affiliation(s)
- Eun Seon Chung
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, MA, USA
| | - Prathitha Kar
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Maliwan Kamkaew
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, MA, USA
| | - Ariel Amir
- Department of Complex Systems, Weizmann Institute of Science, Rehovot, Israel.
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, MA, USA.
- Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA, USA.
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32
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Ripandelli RA, Mueller SH, Robinson A, van Oijen AM. A Single-Cell Interrogation System from Scratch: Microfluidics and Deep Learning. J Phys Chem B 2024; 128:11501-11515. [PMID: 39547656 PMCID: PMC11613446 DOI: 10.1021/acs.jpcb.4c02745] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 09/08/2024] [Accepted: 09/10/2024] [Indexed: 11/17/2024]
Abstract
Live-cell imaging using fluorescence microscopy enables researchers to study cellular processes in unprecedented detail. These techniques are becoming increasingly popular among microbiologists. The emergence of microfluidics and deep learning has significantly increased the amount of quantitative data that can be extracted from such experiments. However, these techniques require highly specialized expertise and equipment, making them inaccessible to many biologists. Here we present a guide for microbiologists, with a basic understanding of microfluidics, to construct a custom-made live-cell interrogation system that is capable of recording and analyzing thousands of bacterial cell-cycles per experiment. The requirements for different microbiological applications are varied, and experiments often demand a high level of versatility and custom-designed capabilities. This work is intended as a guide for the design and engineering of microfluidic master molds and how to build polydimethylsiloxane chips. Furthermore, we show how state-of-the-art deep-learning techniques can be used to design image processing algorithms that allow for the rapid extraction of highly quantitative information from large populations of individual bacterial cells.
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33
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Alnahhas RN, Andreani V, Dunlop MJ. Evaluating the predictive power of combined gene expression dynamics from single cells on antibiotic survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.23.624989. [PMID: 39651301 PMCID: PMC11623535 DOI: 10.1101/2024.11.23.624989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2024]
Abstract
Heteroresistance can allow otherwise drug-susceptible bacteria to survive and resume growth after antibiotic exposure. This temporary form of antibiotic tolerance can be caused by the upregulation of stress response genes or a decrease in cell growth rate. However, it is not clear how expression of multiple genes contributes to the tolerance phenotype. By using fluorescent reporters for stress related genes, we conducted real time measurements of expression prior to, during, and after antibiotic exposure. We first identified relationships between growth rate and reporter levels based on auto and cross correlation analysis, revealing consistent patterns where changes in growth rate were anticorrelated with fluorescence following a delay. We then used pairs of stress gene reporters and time lapse fluorescence microcopy to measure the growth rate and reporter levels in cells that survived or died following antibiotic exposure. Using these data, we asked whether combined information about reporter expression and growth rate could improve our ability to predict whether a cell would survive or die following antibiotic exposure. We developed a Bayesian inference model to predict how the combination of dual reporter expression levels and growth rate impact ciprofloxacin survival in Escherichia coli . We found clear evidence of the impact of growth rate and the gadX promoter activity on survival. Unexpectedly, our results also revealed examples where additional information from multiple genes decreased prediction accuracy, highlighting an important and underappreciated effect that can occur when integrating data from multiple simultaneous measurements.
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34
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Keating C, Fiege K, Diender M, Sousa DZ, Villanueva L. Microbial single-cell applications under anoxic conditions. Appl Environ Microbiol 2024; 90:e0132124. [PMID: 39345115 PMCID: PMC11577760 DOI: 10.1128/aem.01321-24] [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] [Indexed: 10/01/2024] Open
Abstract
The field of microbiology traditionally focuses on studying microorganisms at the population level. Nevertheless, the application of single-cell level methods, including microfluidics and imaging techniques, has revealed heterogeneity within populations, making these methods essential to understand cellular activities and interactions at a higher resolution. Moreover, single-cell sorting has opened new avenues for isolating cells of interest from microbial populations or complex microbial communities. These isolated cells can be further interrogated in downstream single-cell "omics" analyses, providing physiological and functional information. However, applying these methods to study anaerobic microorganisms under in situ conditions remains challenging due to their sensitivity to oxygen. Here, we review the existing methodologies for the analysis of viable anaerobic microorganisms at the single-cell level, including live-imaging, cell sorting, and microfluidics (lab-on-chip) applications, and we address the challenges involved in their anoxic operation. Additionally, we discuss the development of non-destructive imaging techniques tailored for anaerobes, such as oxygen-independent fluorescent probes and alternative approaches.
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Affiliation(s)
- Ciara Keating
- Department of Engineering, Durham University, Durham, United Kingdom
| | - Kerstin Fiege
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Den Burg, the Netherlands
| | - Martijn Diender
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, the Netherlands
| | - Diana Z. Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, the Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Den Burg, the Netherlands
- Department of Biology, Utrecht University, Utrecht, the Netherlands
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35
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Chao L, Chan CK, Shi C, Rang UC. Spatial and temporal distribution of ribosomes in single cells reveals aging differences between old and new daughters of Escherichia coli. eLife 2024; 12:RP89543. [PMID: 39565213 DOI: 10.7554/elife.89543] [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] [Indexed: 11/21/2024] Open
Abstract
Lineages of rod-shaped bacteria such as Escherichia coli exhibit a temporal decline in elongation rate in a manner comparable to cellular or biological aging. The effect results from the production of asymmetrical daughters, one with a lower elongation rate, by the division of a mother cell. The slower daughter compared to the faster daughter, denoted respectively as the old and new daughters, has more aggregates of damaged proteins and fewer expressed gene products. We have examined further the degree of asymmetry by measuring the density of ribosomes between old and new daughters and between their poles. We found that ribosomes were denser in the new daughter and also in the new pole of the daughters. These ribosome patterns match the ones we previously found for expressed gene products. This outcome suggests that the asymmetry is not likely to result from properties unique to the gene expressed in our previous study, but rather from a more fundamental upstream process affecting the distribution of ribosomal abundance. Because damage aggregates and ribosomes are both more abundant at the poles of E. coli cells, we suggest that competition for space between the two could explain the reduced ribosomal density in old daughters. Using published values for aggregate sizes and the relationship between ribosomal number and elongation rates, we show that the aggregate volumes could in principle displace quantitatively the amount of ribosomes needed to reduce the elongation rate of the old daughters.
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Affiliation(s)
- Lin Chao
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, United States
| | - Chun Kuen Chan
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, United States
| | - Chao Shi
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, United States
| | - Ulla Camilla Rang
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, La Jolla, United States
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36
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Proenca AM, Tuğrul M, Nath A, Steiner UK. Progressive decline in old pole gene expression signal enhances phenotypic heterogeneity in bacteria. SCIENCE ADVANCES 2024; 10:eadp8784. [PMID: 39514668 PMCID: PMC11546803 DOI: 10.1126/sciadv.adp8784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 10/07/2024] [Indexed: 11/16/2024]
Abstract
Cell growth and gene expression are heterogeneous processes at the single-cell level, leading to the emergence of multiple physiological states within bacterial populations. Aging is a known deterministic driver of growth asymmetry; however, its role in gene expression heterogeneity remains elusive. Here, we show that aging mother cells undergo a progressive decline in old pole activity, generating asymmetry in protein partitioning, gene expression, and cell morphology. We demonstrate that mother cells, when compared to their daughters, exhibit lower product inheritance and gene expression rates independently of promoter dynamics. The declining activity of maternal old poles generates gene expression gradients that manifest as mother-daughter asymmetry upon division, showing that asymmetry is progressively built over time within the maternal intracellular environment. Moreover, old pole aging correlates with a gradual increase in cell length, leading to morphological asymmetry. These findings provide further evidence for aging as a mechanism to enhance phenotypic heterogeneity in bacterial populations, with possible consequences for stress response and survival.
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Affiliation(s)
- Audrey M. Proenca
- Institute of Biology, Evolutionary Demography Group, Freie Universität Berlin, Königin-Luise-Str. 1-3, 14195 Berlin, Germany
| | - Murat Tuğrul
- Institute of Biology, Evolutionary Demography Group, Freie Universität Berlin, Königin-Luise-Str. 1-3, 14195 Berlin, Germany
| | - Arpita Nath
- Institute of Biology, Evolutionary Demography Group, Freie Universität Berlin, Königin-Luise-Str. 1-3, 14195 Berlin, Germany
| | - Ulrich K. Steiner
- Institute of Biology, Evolutionary Demography Group, Freie Universität Berlin, Königin-Luise-Str. 1-3, 14195 Berlin, Germany
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37
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Wang Q, Wang J, Chen YP, Shen Y, Yan P. Scavenging of reactive oxygen species in Candidatus Brocadia fulgida through nanocompartments. BIORESOURCE TECHNOLOGY 2024; 411:131348. [PMID: 39182796 DOI: 10.1016/j.biortech.2024.131348] [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: 05/19/2024] [Revised: 08/22/2024] [Accepted: 08/22/2024] [Indexed: 08/27/2024]
Abstract
The antioxidant defense mechanisms for anaerobic ammonia oxidation (anammox) bacteria are still unclear. In this study, the potential antioxidant ability of nanocompartments in Candidatus Brocadia fulgida to typical reactive oxygen species (ROS) was investigated. The results showed that the copies of genes involved in anammox central metabolism were inhibited with hydrogen peroxide (H2O2), while the genes encoded putative anti-oxidative protein (nanocompartments and cargo HAO) up-regulated. The genetically engineered bacteria grew better and maintained the lower ROS levels (65.60 %-78.07 %) and higher electron transport activities (∼5-21 times) than the wild bacteria under H2O2 stimulus. Molecular docking confirmed that nanocompartment proteins could provide diverse sites to bind with H2O2 based on heme as the redox center. Additionally, the nanocompartments induced up-regulation of multiple protective pathways for coping with oxidative stress from H2O2, including antioxidant enzymes and other non-enzymatic pathways. Thus, the heme-containing nanocompartments presented great potential in preventing and relieving oxidative stress.
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Affiliation(s)
- Que Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Jin Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yu Shen
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
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Ripandelli RA, van Oijen AM, Robinson A. Single-Cell Microfluidics: A Primer for Microbiologists. J Phys Chem B 2024; 128:10311-10328. [PMID: 39400277 PMCID: PMC11514030 DOI: 10.1021/acs.jpcb.4c02746] [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: 04/29/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 10/15/2024]
Abstract
Recent advances in microfluidic technology have made it possible to image live bacterial cells with a high degree of precision and control. In particular, single-cell microfluidic designs have created new opportunities to study phenotypic variation in bacterial populations. However, the development and use of microfluidic devices require specialized resources, and these can be practical barriers to entry for microbiologists. With this review, our intentions are to help demystify the design, construction, and application of microfluidics. Our approach is to present design elements as building blocks from which a multitude of microfluidics applications can be imagined by the microbiologist.
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Pollack-Milgate S, Saitia S, Tang JX. Rapid growth rate of Enterobacter sp. SM3 determined using several methods. BMC Microbiol 2024; 24:403. [PMID: 39390418 PMCID: PMC11465882 DOI: 10.1186/s12866-024-03547-3] [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: 09/26/2023] [Accepted: 09/25/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Bacterial growth rate, commonly reported in terms of doubling time, is frequently determined by one of two techniques: either by measuring optical absorption of a growing culture or by taking samples at different times during their growth phase, diluting them, spreading them on agar plates, incubating them, and counting the colonies that form. Both techniques require measurements of multiple repeats, as well careful assessment of reproducibility and consistency. Existing literature using either technique gives a wide range of growth rate values for even the most extensively studied species of bacteria, such as Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. This work aims to apply several methods to reliably determine the growth rate of a recently identified species of Enterobacteriaceae, called Enterobacter sp. SM3, and to compare that rate with that of a well-known wildtype E. coli strain KP437. RESULTS We extend conventional optical density (OD) measurements to determine the growth rate of Enterobacter sp. SM3. To assess the reliability of this technique, we compare growth rates obtained by fitting the OD data to exponential growth, applying a relative density method, and measuring shifts in OD curves following set factors of dilution. The main source of error in applying the OD technique is due to the reliance on an exponential growth phase with a short span. With proper choice of parameter range, however, we show that these three methods yield consistent results. We also measured the SM3 division rate by counting colony-forming units (CFU) versus time, yielding results consistent with the OD measurements. In lysogeny broth at 37oC, SM3 divides every 21 ± 3 min, notably faster than the RP437 strain of E. coli, which divides every 29 ± 2 min. CONCLUSION The main conclusion of this report is that conventional optical density (OD) measurements and the colony-forming units (CFU) method can yield consistent values of bacterial growth rate. However, to ensure the reproducibility and reliability of the measured growth rate of each bacterial strain, different methods ought to be applied in close comparison. The effort of checking for consistency among multiple techniques, as we have done in this study, is necessary to avoid reporting variable values of doubling time for particular species or strains of bacteria, as seen in the literature.
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Affiliation(s)
| | - Sanchi Saitia
- Department of Physics, Brown University, 182 Hope Street, Providence, RI, 02912, USA
| | - Jay X Tang
- Department of Physics, Brown University, 182 Hope Street, Providence, RI, 02912, USA.
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40
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Ritz D, Deng Y, Schultz D. Common regulatory mutation increases single-cell survival to antibiotic exposures in Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.20.614194. [PMID: 39345531 PMCID: PMC11430049 DOI: 10.1101/2024.09.20.614194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Typical antibiotic susceptibility testing (AST) of microbial samples is performed in homogeneous cultures in steady environments, which does not account for the highly heterogeneous and dynamic nature of antibiotic responses. The most common mutation found in P. aeruginosa lineages evolved in the human lung, a loss of function of repressor MexZ, increases basal levels of multidrug efflux MexXY, but does not increase resistance by traditional MIC measures. Here, we use single cell microfluidics to show that P. aeruginosa response to aminoglycosides is highly heterogeneous, with only a subpopulation of cells surviving exposure. mexZ mutations then bypass the lengthy process of MexXY activation, increasing survival to sudden drug exposures and conferring a fitness advantage in fluctuating environments. We propose a simple "Response Dynamics" assay to quantify the speed of population-level recovery to drug exposures. This assay can be used alongside MIC for resistance profiling to better predict clinical outcomes.
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Affiliation(s)
- David Ritz
- Department of Microbiology & Immunology, Geisel School of Medicine, Hanover, NH 03755, USA
| | - Yijie Deng
- Thayer School of Engineering – Dartmouth College, Hanover, NH 03755, USA
| | - Daniel Schultz
- Department of Microbiology & Immunology, Geisel School of Medicine, Hanover, NH 03755, USA
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41
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Liguori F, Pellicciotta N, Milanetti E, Xi Windemuth S, Ruocco G, Di Leonardo R, Danino T. Dynamic Gene Expression Mitigates Mutational Escape in Lysis-Driven Bacteria Cancer Therapy. BIODESIGN RESEARCH 2024; 6:0049. [PMID: 39301524 PMCID: PMC11411163 DOI: 10.34133/bdr.0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/09/2024] [Accepted: 08/25/2024] [Indexed: 09/22/2024] Open
Abstract
Engineered bacteria have the potential to deliver therapeutic payloads directly to tumors, with synthetic biology enabling precise control over therapeutic release in space and time. However, it remains unclear how to optimize therapeutic bacteria for durable colonization and sustained payload release. Here, we characterize nonpathogenic Escherichia coli expressing the bacterial toxin Perfringolysin O (PFO) and dynamic strategies that optimize therapeutic efficacy. While PFO is known for its potent cancer cell cytotoxicity, we present experimental evidence that expression of PFO causes lysis of bacteria in both batch culture and microfluidic systems, facilitating its efficient release. However, prolonged expression of PFO leads to the emergence of a mutant population that limits therapeutic-releasing bacteria in a PFO expression level-dependent manner. We present sequencing data revealing the mutant takeover and employ molecular dynamics to confirm that the observed mutations inhibit the lysis efficiency of PFO. To analyze this further, we developed a mathematical model describing the evolution of therapeutic-releasing and mutant bacteria populations revealing trade-offs between therapeutic load delivered and fraction of mutants that arise. We demonstrate that a dynamic strategy employing short and repeated inductions of the pfo gene better preserves the original population of therapeutic bacteria by mitigating the effects of mutational escape. Altogether, we demonstrate how dynamic modulation of gene expression can address mutant takeovers giving rise to limitations in engineered bacteria for therapeutic applications.
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Affiliation(s)
- Filippo Liguori
- Department of Physics, Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Nicola Pellicciotta
- NANOTEC-CNR, Soft and Living Matter Laboratory, Institute of Nanotechnology, Rome, Italy
- Department of Physics, Sapienza University of Rome, Rome, Italy
| | - Edoardo Milanetti
- Department of Physics, Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Sophia Xi Windemuth
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Giancarlo Ruocco
- Department of Physics, Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Roberto Di Leonardo
- Department of Physics, Sapienza University of Rome, Rome, Italy
- NANOTEC-CNR, Soft and Living Matter Laboratory, Institute of Nanotechnology, Rome, Italy
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
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Atasoy M, Bartkova S, Çetecioğlu-Gürol Z, P Mira N, O'Byrne C, Pérez-Rodríguez F, Possas A, Scheler O, Sedláková-Kaduková J, Sinčák M, Steiger M, Ziv C, Lund PA. Methods for studying microbial acid stress responses: from molecules to populations. FEMS Microbiol Rev 2024; 48:fuae015. [PMID: 38760882 PMCID: PMC11418653 DOI: 10.1093/femsre/fuae015] [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: 07/04/2023] [Revised: 03/27/2024] [Accepted: 05/16/2024] [Indexed: 05/20/2024] Open
Abstract
The study of how micro-organisms detect and respond to different stresses has a long history of producing fundamental biological insights while being simultaneously of significance in many applied microbiological fields including infection, food and drink manufacture, and industrial and environmental biotechnology. This is well-illustrated by the large body of work on acid stress. Numerous different methods have been used to understand the impacts of low pH on growth and survival of micro-organisms, ranging from studies of single cells to large and heterogeneous populations, from the molecular or biophysical to the computational, and from well-understood model organisms to poorly defined and complex microbial consortia. Much is to be gained from an increased general awareness of these methods, and so the present review looks at examples of the different methods that have been used to study acid resistance, acid tolerance, and acid stress responses, and the insights they can lead to, as well as some of the problems involved in using them. We hope this will be of interest both within and well beyond the acid stress research community.
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Affiliation(s)
- Merve Atasoy
- UNLOCK, Wageningen University and Research, PO Box 9101, 6700 HB, the Netherlands
| | - Simona Bartkova
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Zeynep Çetecioğlu-Gürol
- Department of Industrial Biotechnology, KTH Royal Institute of Technology, Roslagstullsbacken 21 106 91 Stockholm, Stockholm, Sweden
| | - Nuno P Mira
- iBB, Institute for Bioengineering and Biosciences, Department of Bioengineering, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Conor O'Byrne
- Microbiology, School of Biological and Chemical Sciences, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Fernando Pérez-Rodríguez
- Department of Food Science and Tehcnology, UIC Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, 14014 Córdoba, Spain
| | - Aricia Possas
- Department of Food Science and Tehcnology, UIC Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, 14014 Córdoba, Spain
| | - Ott Scheler
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Jana Sedláková-Kaduková
- Institute of Chemistry and Environmental Sciences, University of Ss. Cyril and Methodius, 91701 Trnava, Republic of Slovakia
| | - Mirka Sinčák
- Institute of Chemistry and Environmental Sciences, University of Ss. Cyril and Methodius, 91701 Trnava, Republic of Slovakia
| | - Matthias Steiger
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Carmit Ziv
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, 7505101 Rishon LeZion, Israel
| | - Peter A Lund
- School of Biosciences and Institute of Microbiology of Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
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Hardo G, Li R, Bakshi S. Quantitative microbiology with widefield microscopy: navigating optical artefacts for accurate interpretations. NPJ IMAGING 2024; 2:26. [PMID: 39234390 PMCID: PMC11368818 DOI: 10.1038/s44303-024-00024-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 06/21/2024] [Indexed: 09/06/2024]
Abstract
Time-resolved live-cell imaging using widefield microscopy is instrumental in quantitative microbiology research. It allows researchers to track and measure the size, shape, and content of individual microbial cells over time. However, the small size of microbial cells poses a significant challenge in interpreting image data, as their dimensions approache that of the microscope's depth of field, and they begin to experience significant diffraction effects. As a result, 2D widefield images of microbial cells contain projected 3D information, blurred by the 3D point spread function. In this study, we employed simulations and targeted experiments to investigate the impact of diffraction and projection on our ability to quantify the size and content of microbial cells from 2D microscopic images. This study points to some new and often unconsidered artefacts resulting from the interplay of projection and diffraction effects, within the context of quantitative microbiology. These artefacts introduce substantial errors and biases in size, fluorescence quantification, and even single-molecule counting, making the elimination of these errors a complex task. Awareness of these artefacts is crucial for designing strategies to accurately interpret micrographs of microbes. To address this, we present new experimental designs and machine learning-based analysis methods that account for these effects, resulting in accurate quantification of microbiological processes.
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Affiliation(s)
- Georgeos Hardo
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - Ruizhe Li
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - Somenath Bakshi
- Department of Engineering, University of Cambridge, Cambridge, UK
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Zhao X, Ying J, Wang Z, Wang Y, Li Z, Gu T, Liu S, Li Y, Liu B, Xin F, Wen B. In vitro digestive properties and the bioactive effect of walnut green husk on human gut microbiota. Front Microbiol 2024; 15:1392774. [PMID: 39224223 PMCID: PMC11367867 DOI: 10.3389/fmicb.2024.1392774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction Walnut green husk (WGH) is a waste byproduct from walnut industry. However, it is not well-known about its bioactive effect on human gut health. Methods This study conducted in vitro digestion and fermentation experiments to study the bioactive effect of WGH. Results Microbial fermentation was the primary mechanism to efficiently release phenolics and flavonoids, resulting in more excellent antioxidant capacities (DPPH, ABTS, and FRAP assays), which reached a highest value with 14.82 ± 0.01 mg VcE/g DW, 3.47 ± 0.01 mmol TE/g DW, and 0.96 ± 0.07 mmol FeSO4·7H2O/g DW, respectively. The surface microstructure of WGH became loose and fragmented after microbial fermentation. The analytical results of gut microbiota demonstrated that WGH could significantly increase the relative abundance of Proteobacteria in phylum level and Phascolarctobacterium in genus level while certain pro-inflammatory bacteria (such as Clostridium_sensu_stricto_1, Dorea, Alistipes, and Bilophila) was inhibited. Additionally, 1,373 differential metabolites were identified and enriched in 283 KEGG pathways. Of which some metabolites were significantly upregulated including ferulic acid, chlorogenic acid, umbelliferone, scopolin, muricholic acid, and so forth. Discussion These results indicated that WGH could have antioxidant and anti-inflammatory activities in the human gut, which could improve the economical value of WGH in the food industry.
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Affiliation(s)
- Xiaolan Zhao
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Jiabao Ying
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Zhuochen Wang
- Institute of Agro-Products Processing, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yulu Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Zhen Li
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Tianyi Gu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Shujun Liu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yulong Li
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Bing Liu
- Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Fengjiao Xin
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Laboratory of Biomanufacturing and Food Engineering, Institute of Agricultural Product Processing and Nutritional Health, Chinese Academy of Agricultural Sciences (CAAS), Cangzhou, China
| | - Boting Wen
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Laboratory of Biomanufacturing and Food Engineering, Institute of Agricultural Product Processing and Nutritional Health, Chinese Academy of Agricultural Sciences (CAAS), Cangzhou, China
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45
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Boesen TO, Charbon G, Fu H, Jensen C, Sandler M, Jun S, Løbner-Olesen A. Dispensability of extrinsic DnaA regulators in Escherichia coli cell-cycle control. Proc Natl Acad Sci U S A 2024; 121:e2322772121. [PMID: 40014855 PMCID: PMC11331064 DOI: 10.1073/pnas.2322772121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/26/2024] [Indexed: 03/01/2025] Open
Abstract
Investigating a long-standing conceptual question in bacterial physiology, we examine why DnaA, the bacterial master replication initiator protein, exists in both ATP and ADP forms, despite only the ATP form being essential for initiation. We engineered the Δ4 Escherichia coli strain, devoid of all known external elements facilitating the DnaA-ATP/ADP conversion and found that these cells display nearly wild-type behaviors under nonoverlapping replication cycles. However, during rapid growth with overlapping cycles, Δ4 cells exhibit initiation instability. This aligns with our model predictions, suggesting that the intrinsic ATPase activity of DnaA alone is sufficient for robust initiation control in E. coli and the DnaA-ATP/ADP conversion regulatory elements extend the robustness to multifork replication, indicating an evolutionary adaptation. Moreover, our experiments revealed constant DnaA concentrations during steady-state cell elongation in both wild-type and Δ4 cells. These insights not only advance our understanding of bacterial cell-cycle regulation and DnaA but also highlight a fundamental divergence from eukaryotic cell-cycle controls, emphasizing protein copy-number sensing in bacteria versus programmed protein concentration oscillations in eukaryotes.
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Affiliation(s)
- Thias Oberg Boesen
- Department of Biology, University of Copenhagen, Copenhagen2200, Denmark
| | - Godefroid Charbon
- Department of Biology, University of Copenhagen, Copenhagen2200, Denmark
| | - Haochen Fu
- Department of Physics, University of California San Diego, La Jolla, CA92093
| | - Cara Jensen
- Department of Physics, University of California San Diego, La Jolla, CA92093
| | - Michael Sandler
- Department of Physics, University of California San Diego, La Jolla, CA92093
| | - Suckjoon Jun
- Department of Physics, University of California San Diego, La Jolla, CA92093
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Ascensao JA, Lok K, Hallatschek O. Asynchronous abundance fluctuations can drive giant genotype frequency fluctuations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.23.581776. [PMID: 38562700 PMCID: PMC10983864 DOI: 10.1101/2024.02.23.581776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Large stochastic population abundance fluctuations are ubiquitous across the tree of life1-7, impacting the predictability of population dynamics and influencing eco-evolutionary outcomes. It has generally been thought that these large abundance fluctuations do not strongly impact evolution, as the relative frequencies of alleles in the population will be unaffected if the abundance of all alleles fluctuate in unison. However, we argue that large abundance fluctuations can lead to significant genotype frequency fluctuations if different genotypes within a population experience these fluctuations asynchronously. By serially diluting mixtures of two closely related E. coli strains, we show that such asynchrony can occur, leading to giant frequency fluctuations that far exceed expectations from models of genetic drift. We develop a flexible, effective model that explains the abundance fluctuations as arising from correlated offspring numbers between individuals, and the large frequency fluctuations result from even slight decoupling in offspring numbers between genotypes. This model accurately describes the observed abundance and frequency fluctuation scaling behaviors. Our findings suggest chaotic dynamics underpin these giant fluctuations, causing initially similar trajectories to diverge exponentially; subtle environmental changes can be magnified, leading to batch correlations in identical growth conditions. Furthermore, we present evidence that such decoupling noise is also present in mixed-genotype S. cerevisiae populations. We demonstrate that such decoupling noise can strongly influence evolutionary outcomes, in a manner distinct from genetic drift. Given the generic nature of asynchronous fluctuations, we anticipate that they are widespread in biological populations, significantly affecting evolutionary and ecological dynamics.
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Affiliation(s)
- Joao A Ascensao
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA, USA
| | - Kristen Lok
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
- Present affiliation: Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Oskar Hallatschek
- Department of Physics, University of California Berkeley, Berkeley, CA, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
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Le Quellec L, Aristov A, Gutiérrez Ramos S, Amselem G, Bos J, Baharoglu Z, Mazel D, Baroud CN. Measuring single-cell susceptibility to antibiotics within monoclonal bacterial populations. PLoS One 2024; 19:e0303630. [PMID: 39088440 PMCID: PMC11293721 DOI: 10.1371/journal.pone.0303630] [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: 02/19/2024] [Accepted: 04/30/2024] [Indexed: 08/03/2024] Open
Abstract
The emergence of new resistant bacterial strains is a worldwide challenge. A resistant bacterial population can emerge from a single cell that acquires resistance or persistence. Hence, new ways of tackling the mechanism of antibiotic response, such as single cell studies are required. It is necessary to see what happens at the single cell level, in order to understand what happens at the population level. To date, linking the heterogeneity of single-cell susceptibility to the population-scale response to antibiotics remains challenging due to the trade-offs between the resolution and the field of view. Here we present a platform that measures the ability of individual E. coli cells to form small colonies at different ciprofloxacin concentrations, by using anchored microfluidic drops and an image and data analysis pipelines. The microfluidic results are benchmarked against classical microbiology measurements of antibiotic susceptibility, showing an agreement between the pooled microfluidic chip and replated bulk measurements. Further, the experimental likelihood of a single cell to form a colony is used to provide a probabilistic antibiotic susceptibility curve. In addition to the probabilistic viewpoint, the microfluidic format enables the characterization of morphological features over time for a large number of individual cells. This pipeline can be used to compare the response of different bacterial strains to antibiotics with different action mechanisms.
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Affiliation(s)
- Lena Le Quellec
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Andrey Aristov
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris, France
| | - Salomé Gutiérrez Ramos
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Gabriel Amselem
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Julia Bos
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Bacterial Genome Plasticity Unit, Paris, France
| | - Zeynep Baharoglu
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Bacterial Genome Plasticity Unit, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Bacterial Genome Plasticity Unit, Paris, France
| | - Charles N. Baroud
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
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Delprat M, Guarino R, Jordier N, Paulet É, Vedrine L, Aussel L. [Single-cell study in microbiology]. Med Sci (Paris) 2024; 40:692-696. [PMID: 39303126 DOI: 10.1051/medsci/2024119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024] Open
Affiliation(s)
- Manon Delprat
- Master 2 Microbiologie Intégrative et Fondamentale, Aix-Marseille Université, Marseille, France
| | - Romane Guarino
- Master 2 Microbiologie Intégrative et Fondamentale, Aix-Marseille Université, Marseille, France
| | - Nathan Jordier
- Master 2 Microbiologie Intégrative et Fondamentale, Aix-Marseille Université, Marseille, France
| | - Éloïse Paulet
- Master 2 Microbiologie Intégrative et Fondamentale, Aix-Marseille Université, Marseille, France
| | - Léa Vedrine
- Master 2 Microbiologie Intégrative et Fondamentale, Aix-Marseille Université, Marseille, France
| | - Laurent Aussel
- Aix-Marseille Université, CNRS, LCB UMR7283, IMM, Marseille, France
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Kollerová S, Jouvet L, Smelková J, Zunk-Parras S, Rodríguez-Rojas A, Steiner UK. Phenotypic resistant single-cell characteristics under recurring ampicillin antibiotic exposure in Escherichia coli. mSystems 2024; 9:e0025624. [PMID: 38920373 PMCID: PMC11264686 DOI: 10.1128/msystems.00256-24] [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: 02/22/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024] Open
Abstract
Non-heritable, phenotypic drug resistance toward antibiotics challenges antibiotic therapies. Characteristics of such phenotypic resistance have implications for the evolution of heritable resistance. Diverse forms of phenotypic resistance have been described, but phenotypic resistance characteristics remain less explored than genetic resistance. Here, we add novel combinations of single-cell characteristics of phenotypic resistant E. coli cells and compare those to characteristics of susceptible cells of the parental population by exposure to different levels of recurrent ampicillin antibiotic. Contrasting expectations, we did not find commonly described characteristics of phenotypic resistant cells that arrest growth or near growth. We find that under ampicillin exposure, phenotypic resistant cells reduced their growth rate by about 50% compared to growth rates prior to antibiotic exposure. The growth reduction is a delayed alteration to antibiotic exposure, suggesting an induced response and not a stochastic switch or caused by a predetermined state as frequently described. Phenotypic resistant cells exhibiting constant slowed growth survived best under ampicillin exposure and, contrary to expectations, not only fast-growing cells suffered high mortality triggered by ampicillin but also growth-arrested cells. Our findings support diverse modes of phenotypic resistance, and we revealed resistant cell characteristics that have been associated with enhanced genetically fixed resistance evolution, which supports claims of an underappreciated role of phenotypic resistant cells toward genetic resistance evolution. A better understanding of phenotypic resistance will benefit combatting genetic resistance by developing and engulfing effective anti-phenotypic resistance strategies. IMPORTANCE Antibiotic resistance is a major challenge for modern medicine. Aside from genetic resistance to antibiotics, phenotypic resistance that is not heritable might play a crucial role for the evolution of antibiotic resistance. Using a highly controlled microfluidic system, we characterize single cells under recurrent exposure to antibiotics. Fluctuating antibiotic exposure is likely experienced under common antibiotic therapies. These phenotypic resistant cell characteristics differ from previously described phenotypic resistance, highlighting the diversity of modes of resistance. The phenotypic characteristics of resistant cells we identify also imply that such cells might provide a stepping stone toward genetic resistance, thereby causing treatment failure.
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Affiliation(s)
- Silvia Kollerová
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Lionel Jouvet
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Julia Smelková
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | | | | | - Ulrich K. Steiner
- Department of Biology, University of Southern Denmark, Odense, Denmark
- Biological Institute, Freie Universität Berlin, Berlin, Germany
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Ábrahám Á, Dér L, Csákvári E, Vizsnyiczai G, Pap I, Lukács R, Varga-Zsíros V, Nagy K, Galajda P. Single-cell level LasR-mediated quorum sensing response of Pseudomonas aeruginosa to pulses of signal molecules. Sci Rep 2024; 14:16181. [PMID: 39003361 PMCID: PMC11246452 DOI: 10.1038/s41598-024-66706-6] [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: 09/04/2023] [Accepted: 07/03/2024] [Indexed: 07/15/2024] Open
Abstract
Quorum sensing (QS) is a communication form between bacteria via small signal molecules that enables global gene regulation as a function of cell density. We applied a microfluidic mother machine to study the kinetics of the QS response of Pseudomonas aeruginosa bacteria to additions and withdrawals of signal molecules. We traced the fast buildup and the subsequent considerably slower decay of a population-level and single-cell-level QS response. We applied a mathematical model to explain the results quantitatively. We found significant heterogeneity in QS on the single-cell level, which may result from variations in quorum-controlled gene expression and protein degradation. Heterogeneity correlates with cell lineage history, too. We used single-cell data to define and quantitatively characterize the population-level quorum state. We found that the population-level QS response is well-defined. The buildup of the quorum is fast upon signal molecule addition. At the same time, its decay is much slower following signal withdrawal, and the quorum may be maintained for several hours in the absence of the signal. Furthermore, the quorum sensing response of the population was largely repeatable in subsequent pulses of signal molecules.
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Affiliation(s)
- Ágnes Ábrahám
- HUN-REN Biological Research Centre, Institute of Biophysics, Temesvári Krt. 62, Szeged, 6726, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Dóm Tér 9, Szeged, 6720, Hungary
| | - László Dér
- HUN-REN Biological Research Centre, Institute of Biophysics, Temesvári Krt. 62, Szeged, 6726, Hungary
| | - Eszter Csákvári
- HUN-REN Biological Research Centre, Institute of Biophysics, Temesvári Krt. 62, Szeged, 6726, Hungary
- Division for Biotechnology, Bay Zoltán Nonprofit Ltd. for Applied Research, Derkovits Fasor 2., Szeged, 6726, Hungary
| | - Gaszton Vizsnyiczai
- HUN-REN Biological Research Centre, Institute of Biophysics, Temesvári Krt. 62, Szeged, 6726, Hungary
| | - Imre Pap
- HUN-REN Biological Research Centre, Institute of Biophysics, Temesvári Krt. 62, Szeged, 6726, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Dóm Tér 9, Szeged, 6720, Hungary
| | - Rebeka Lukács
- HUN-REN Biological Research Centre, Institute of Biophysics, Temesvári Krt. 62, Szeged, 6726, Hungary
| | - Vanda Varga-Zsíros
- HUN-REN Biological Research Centre, Institute of Biophysics, Temesvári Krt. 62, Szeged, 6726, Hungary
- HUN-REN Biological Research Centre, Institute of Biochemistry, Temesvári Krt. 62, Szeged, 6726, Hungary
| | - Krisztina Nagy
- HUN-REN Biological Research Centre, Institute of Biophysics, Temesvári Krt. 62, Szeged, 6726, Hungary.
| | - Péter Galajda
- HUN-REN Biological Research Centre, Institute of Biophysics, Temesvári Krt. 62, Szeged, 6726, Hungary.
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