1
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Iuliani I, Mbemba G, Lagomarsino MC, Sclavi B. Direct single-cell observation of a key Escherichia coli cell-cycle oscillator. SCIENCE ADVANCES 2024; 10:eado5398. [PMID: 39018394 PMCID: PMC466948 DOI: 10.1126/sciadv.ado5398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 06/10/2024] [Indexed: 07/19/2024]
Abstract
Initiation of DNA replication in Escherichia coli is coupled to cell size via the DnaA protein, whose activity is dependent on its nucleotide-bound state. However, the oscillations in DnaA activity have never been observed at the single-cell level. By measuring the volume-specific production rate of a reporter protein under control of a DnaA-regulated promoter, we could distinguish two distinct cell-cycle oscillators. The first, driven by both DnaA activity and SeqA repression, shows a causal relationship with cell size and divisions, similarly to initiation events. The second one, a reporter of DnaA activity alone, loses the synchrony and causality properties. Our results show that transient inhibition of gene expression by SeqA keeps the oscillation of volume-sensing DnaA activity in phase with the subsequent division event and suggest that DnaA activity peaks do not correspond directly to initiation events.
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Affiliation(s)
- Ilaria Iuliani
- LBPA, UMR 8113, CNRS, ENS Paris-Saclay, 91190 Gif-sur-Yvette, France
- LCQB, UMR 7238, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
- IFOM ETS—The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Gladys Mbemba
- LBPA, UMR 8113, CNRS, ENS Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Marco Cosentino Lagomarsino
- IFOM ETS—The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
- Dipartimento di Fisica, Università degli Studi di Milano, and I.N.F.N, Via Celoria 16, 20133 Milan, Italy
| | - Bianca Sclavi
- LCQB, UMR 7238, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
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2
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Ziegler KF, Joshi K, Wright CS, Roy S, Caruso W, Biswas RR, Iyer-Biswas S. Scaling of stochastic growth and division dynamics: A comparative study of individual rod-shaped cells in the Mother Machine and SChemostat platforms. Mol Biol Cell 2024; 35:ar78. [PMID: 38598301 PMCID: PMC11238078 DOI: 10.1091/mbc.e23-11-0452] [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: 12/11/2023] [Revised: 03/15/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024] Open
Abstract
Microfluidic platforms enable long-term quantification of stochastic behaviors of individual bacterial cells under precisely controlled growth conditions. Yet, quantitative comparisons of physiological parameters and cell behaviors of different microorganisms in different experimental and device modalities is not available due to experiment-specific details affecting cell physiology. To rigorously assess the effects of mechanical confinement, we designed, engineered, and performed side-by-side experiments under otherwise identical conditions in the Mother Machine (with confinement) and the SChemostat (without confinement), using the latter as the ideal comparator. We established a protocol to cultivate a suitably engineered rod-shaped mutant of Caulobacter crescentus in the Mother Machine and benchmarked the differences in stochastic growth and division dynamics with respect to the SChemostat. While the single-cell growth rate distributions are remarkably similar, the mechanically confined cells in the Mother Machine experience a substantial increase in interdivision times. However, we find that the division ratio distribution precisely compensates for this increase, which in turn reflects identical emergent simplicities governing stochastic intergenerational homeostasis of cell sizes across device and experimental configurations, provided the cell sizes are appropriately mean-rescaled in each condition. Our results provide insights into the nature of the robustness of the bacterial growth and division machinery.
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Affiliation(s)
- Karl F. Ziegler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health, Sciences, Monash University, Clayton/Melbourne, VIC 3800, Australia
| | - Kunaal Joshi
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| | - Charles S. Wright
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Shaswata Roy
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| | - Will Caruso
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| | - Rudro R. Biswas
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| | - Srividya Iyer-Biswas
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
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3
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Microfluidic dose-response platform to track the dynamics of drug response in single mycobacterial cells. Sci Rep 2022; 12:19578. [PMID: 36379978 PMCID: PMC9666435 DOI: 10.1038/s41598-022-24175-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Preclinical analysis of drug efficacy is critical for drug development. However, conventional bulk-cell assays statically assess the mean population behavior, lacking resolution on drug-escaping cells. Inaccurate estimation of efficacy can lead to overestimation of compounds, whose efficacy will not be confirmed in the clinic, or lead to rejection of valuable candidates. Time-lapse microfluidic microscopy is a powerful approach to characterize drugs at high spatiotemporal resolution, but hard to apply on a large scale. Here we report the development of a microfluidic platform based on a pneumatic operating principle, which is scalable and compatible with long-term live-cell imaging and with simultaneous analysis of different drug concentrations. We tested the platform with mycobacterial cells, including the tubercular pathogen, providing the first proof of concept of a single-cell dose-response assay. This dynamic in-vitro model will prove useful to probe the fate of drug-stressed cells, providing improved predictions of drug efficacy in the clinic.
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4
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Colin A, Micali G, Faure L, Cosentino Lagomarsino M, van Teeffelen S. Two different cell-cycle processes determine the timing of cell division in Escherichia coli. eLife 2021; 10:67495. [PMID: 34612203 PMCID: PMC8555983 DOI: 10.7554/elife.67495] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
Cells must control the cell cycle to ensure that key processes are brought to completion. In Escherichia coli, it is controversial whether cell division is tied to chromosome replication or to a replication-independent inter-division process. A recent model suggests instead that both processes may limit cell division with comparable odds in single cells. Here, we tested this possibility experimentally by monitoring single-cell division and replication over multiple generations at slow growth. We then perturbed cell width, causing an increase of the time between replication termination and division. As a consequence, replication became decreasingly limiting for cell division, while correlations between birth and division and between subsequent replication-initiation events were maintained. Our experiments support the hypothesis that both chromosome replication and a replication-independent inter-division process can limit cell division: the two processes have balanced contributions in non-perturbed cells, while our width perturbations increase the odds of the replication-independent process being limiting.
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Affiliation(s)
- Alexandra Colin
- Microbial Morphogenesis and Growth Laboratory, Institut Pasteur, Paris, France
| | - Gabriele Micali
- Department of Environmental Microbiology, Dübendorf, Switzerland.,Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Louis Faure
- Microbial Morphogenesis and Growth Laboratory, Institut Pasteur, Paris, France
| | - Marco Cosentino Lagomarsino
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy.,Physics Department, University of Milan, and INFN, Milan, Italy
| | - Sven van Teeffelen
- Microbial Morphogenesis and Growth Laboratory, Institut Pasteur, Paris, France.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Canada
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5
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Microfluidic Single-Cell Analytics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 179:159-189. [PMID: 32737554 DOI: 10.1007/10_2020_134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
What is the impact of cellular heterogeneity on process performance? How do individual cells contribute to averaged process productivity? Single-cell analysis is a key technology for answering such key questions of biotechnology, beyond bulky measurements with populations. The analysis of cellular individuality, its origins, and the dependency of process performance on cellular heterogeneity has tremendous potential for optimizing biotechnological processes in terms of metabolic, reaction, and process engineering. Microfluidics offer unmatched environmental control of the cellular environment and allow massively parallelized cultivation of single cells. However, the analytical accessibility to a cell's physiology is of crucial importance for obtaining the desired information on the single-cell production phenotype. Highly sensitive analytics are required to detect and quantify the minute amounts of target analytes and small physiological changes in a single cell. For their application to biotechnological questions, single-cell analytics must evolve toward the measurement of kinetics and specific rates of the smallest catalytic unit, the single cell. In this chapter, we focus on an introduction to the latest single-cell analytics and their application for obtaining physiological parameters in a biotechnological context from single cells. We present and discuss recent advancements in single-cell analytics that enable the analysis of cell-specific growth, uptake, and production kinetics, as well as the gene expression and regulatory mechanisms at a single-cell level.
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6
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Xin L, Zeng Y, Sheng S, Chea RA, Liu Q, Li HY, Yang L, Xu L, Chiam KH, Liang ZX. Regulation of flagellar motor switching by c-di-GMP phosphodiesterases in Pseudomonas aeruginosa. J Biol Chem 2019; 294:13789-13799. [PMID: 31350333 DOI: 10.1074/jbc.ra119.009009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/23/2019] [Indexed: 12/12/2022] Open
Abstract
The second messenger cyclic diguanylate (c-di-GMP) plays a prominent role in regulating flagellum-dependent motility in the single-flagellated pathogenic bacterium Pseudomonas aeruginosa The c-di-GMP-mediated signaling pathways and mechanisms that control flagellar output remain to be fully unveiled. Studying surface-tethered and free-swimming P. aeruginosa PAO1 cells, we found that the overexpression of an exogenous diguanylate cyclase (DGC) raises the global cellular c-di-GMP concentration and thereby inhibits flagellar motor switching and decreases motor speed, reducing swimming speed and reversal frequency, respectively. We noted that the inhibiting effect of c-di-GMP on flagellar motor switching, but not motor speed, is exerted through the c-di-GMP-binding adaptor protein MapZ and associated chemotactic pathways. Among the 22 putative c-di-GMP phosphodiesterases, we found that three of them (DipA, NbdA, and RbdA) can significantly inhibit flagellar motor switching and swimming directional reversal in a MapZ-dependent manner. These results disclose a network of c-di-GMP-signaling proteins that regulate chemotactic responses and flagellar motor switching in P. aeruginosa and establish MapZ as a key signaling hub that integrates inputs from different c-di-GMP-signaling pathways to control flagellar output and bacterial motility. We rationalized these experimental findings by invoking a model that postulates the regulation of flagellar motor switching by subcellular c-di-GMP pools.
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Affiliation(s)
- Lingyi Xin
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Yukai Zeng
- Bioinformatics Institute (A*STAR), S138671, Singapore
| | - Shuo Sheng
- Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Rachel Andrea Chea
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Qiong Liu
- Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Hoi Yeung Li
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Liang Yang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.,Interdisciplinary Graduate School, Nanyang Technological University, S637551, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Linghui Xu
- Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China.,Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
| | | | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore .,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
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7
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Yu S, Sheats J, Cicuta P, Sclavi B, Cosentino Lagomarsino M, Dorfman KD. Subdiffusion of loci and cytoplasmic particles are different in compressed Escherichia coli cells. Commun Biol 2018; 1:176. [PMID: 30374466 PMCID: PMC6200837 DOI: 10.1038/s42003-018-0185-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 10/03/2018] [Indexed: 12/13/2022] Open
Abstract
The complex physical nature of the bacterial intracellular environment remains largely unknown, and has relevance for key biochemical and biological processes of the cell. Although recent work has addressed the role of non-equilibrium sources of activity and crowding, the consequences of mechanical perturbations are relatively less explored. Here we use a microfabricated valve system to track both fluorescently labeled chromosomal loci and cytoplasmic particles in Escherichia coli cells shortly after applying a compressive force, observing the response on time scales that are too sudden to allow for biochemical response from the cell. Cytoplasmic diffusion slows markedly on compression but the exponent governing the growth of the ensemble-averaged mean-squared displacement of cytoplasmic particles is unaffected. In contrast, the corresponding exponent for DNA loci changes significantly. These results suggest that DNA elasticity and nucleoid organization play a more important role in loci subdiffusion than cytoplasmic viscoelasticity under such short time scales.
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Affiliation(s)
- Shi Yu
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, MN, 55455, USA
- School of Chemical Engineering and Technology, China University of Mining & Technology, Xuzhou, 221116, China
| | - Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, MN, 55455, USA
| | - Pietro Cicuta
- Cavendish Laboratory, Cambridge University, Cambridge, UK
| | - Bianca Sclavi
- LBPA, UMR 8113 du CNRS, École Normale Supérieure Paris-Saclay, Cachan, France
| | - Marco Cosentino Lagomarsino
- Génophysique/Genomic Physics Group, UMR 7238 CNRS Génomique des Microorganismes, Université Pierre et Marie Curie, 4, Place Jussieu, 75005, Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie, 4 Place Jussieu, Paris, France
- IFOM Institute for Molecular Oncology, Milan, Italy
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, MN, 55455, USA.
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8
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Hsieh K, Zec HC, Chen L, Kaushik AM, Mach KE, Liao JC, Wang TH. Simple and Precise Counting of Viable Bacteria by Resazurin-Amplified Picoarray Detection. Anal Chem 2018; 90:9449-9456. [PMID: 29969556 DOI: 10.1021/acs.analchem.8b02096] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Simple, fast, and precise counting of viable bacteria is fundamental to a variety of microbiological applications such as food quality monitoring and clinical diagnosis. To this end, agar plating, microscopy, and emerging microfluidic devices for single bacteria detection have provided useful means for counting viable bacteria, but they also have their limitations ranging from complexity, time, and inaccuracy. We present herein our new method RAPiD (Resazurin-Amplified Picoarray Detection) for addressing this important problem. In RAPiD, we employ vacuum-assisted sample loading and oil-driven sample digitization to stochastically confine single bacteria in Picoarray, a microfluidic device with picoliter-sized isolation chambers (picochambers), in <30 s with only a few minutes of hands-on time. We add AlamarBlue, a resazurin-based fluorescent dye for bacterial growth, in our assay to accelerate the detection of "microcolonies" proliferated from single bacteria within picochambers. Detecting fluorescence in picochambers as an amplified surrogate for bacterial cells allows us to count hundreds of microcolonies with a single image taken via wide-field fluorescence microscopy. We have also expanded our method to practically test multiple titrations from a single bacterial sample in parallel. Using this expanded "multi-RAPiD" strategy, we can quantify viable cells in E. coli and S. aureus samples with precision in ∼3 h, illustrating RAPiD as a promising new method for counting viable bacteria for microbiological applications.
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Affiliation(s)
- Kuangwen Hsieh
- Department of Mechanical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Helena C Zec
- Department of Biomedical Engineering , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
| | - Liben Chen
- Department of Mechanical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Aniruddha M Kaushik
- Department of Mechanical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Kathleen E Mach
- Department of Urology , Stanford University School of Medicine , Stanford , California 94305 , United States
| | - Joseph C Liao
- Department of Urology , Stanford University School of Medicine , Stanford , California 94305 , United States
| | - Tza-Huei Wang
- Department of Mechanical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States.,Department of Biomedical Engineering , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
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9
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Abstract
Microfluidic technology overcomes many of the limitations to traditional analytical methods in microbiology. Unlike bulk-culture methods, it offers single-cell resolution and long observation times spanning hundreds of generations; unlike agarose pad-based microscopy, it has uniform growth conditions that can be tightly controlled. Because the continuous flow of growth medium isolates the cells in a microfluidic device from unpredictable variations in the local chemical environment caused by cell growth and metabolism, authentic changes in gene expression and cell growth in response to specific stimuli can be more confidently observed. Bacillus subtilis is used here as a model bacterial species to demonstrate a "mother machine"-type method for cellular analysis. We show how to construct and plumb a microfluidic device, load it with cells, initiate microscopic imaging, and expose cells to a stimulus by switching from one growth medium to another. A stress-responsive reporter is used as an example to reveal the type of data that may be obtained by this method. We also briefly discuss further applications of this method for other types of experiments, such as analysis of bacterial sporulation.
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Affiliation(s)
- Matthew T Cabeen
- Department of Microbiology and Molecular Genetics, Oklahoma State University;
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University;
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10
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Kaiser M, Jug F, Julou T, Deshpande S, Pfohl T, Silander OK, Myers G, van Nimwegen E. Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software. Nat Commun 2018; 9:212. [PMID: 29335514 PMCID: PMC5768764 DOI: 10.1038/s41467-017-02505-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/06/2017] [Indexed: 12/16/2022] Open
Abstract
Much is still not understood about how gene regulatory interactions control cell fate decisions in single cells, in part due to the difficulty of directly observing gene regulatory processes in vivo. We introduce here a novel integrated setup consisting of a microfluidic chip and accompanying analysis software that enable long-term quantitative tracking of growth and gene expression in single cells. The dual-input Mother Machine (DIMM) chip enables controlled and continuous variation of external conditions, allowing direct observation of gene regulatory responses to changing conditions in single cells. The Mother Machine Analyzer (MoMA) software achieves unprecedented accuracy in segmenting and tracking cells, and streamlines high-throughput curation with a novel leveraged editing procedure. We demonstrate the power of the method by uncovering several novel features of an iconic gene regulatory program: the induction of Escherichia coli's lac operon in response to a switch from glucose to lactose.
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Affiliation(s)
- Matthias Kaiser
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Florian Jug
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
| | - Thomas Julou
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Siddharth Deshpande
- Department of Chemistry, University of Basel, Spitalstrasse 51, 4056, Basel, Switzerland
- Department of Bionanoscience, TU Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Thomas Pfohl
- Department of Chemistry, University of Basel, Spitalstrasse 51, 4056, Basel, Switzerland
| | - Olin K Silander
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056, Basel, Switzerland.
- Institute of Natural and Mathematical Sciences, Massey University Auckland, Private Bag 102904, North Shore, 0745, New Zealand.
| | - Gene Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany.
| | - Erik van Nimwegen
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056, Basel, Switzerland.
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11
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Yuan X, Couto JM, Glidle A, Song Y, Sloan W, Yin H. Single-Cell Microfluidics to Study the Effects of Genome Deletion on Bacterial Growth Behavior. ACS Synth Biol 2017; 6:2219-2227. [PMID: 28844132 DOI: 10.1021/acssynbio.7b00177] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
By directly monitoring single cell growth in a microfluidic platform, we interrogated genome-deletion effects in Escherichia coli strains. We compared the growth dynamics of a wild type strain with a clean genome strain, and their derived mutants at the single-cell level. A decreased average growth rate and extended average lag time were found for the clean genome strain, compared to those of the wild type strain. Direct correlation between the growth rate and lag time of individual cells showed that the clean genome population was more heterogeneous. Cell culturability (the ratio of growing cells to the sum of growing and nongrowing cells) of the clean genome population was also lower. Interestingly, after the random mutations induced by a glucose starvation treatment, for the clean genome population mutants that had survived the competition of chemostat culture, each parameter markedly improved (i.e., the average growth rate and cell culturability increased, and the lag time and heterogeneity decreased). However, this effect was not seen in the wild type strain; the wild type mutants cultured in a chemostat retained a high diversity of growth phenotypes. These results suggest that quasi-essential genes that were deleted in the clean genome might be required to retain a diversity of growth characteristics at the individual cell level under environmental stress. These observations highlight that single-cell microfluidics can reveal subtle individual cellular responses, enabling in-depth understanding of the population.
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Affiliation(s)
- Xiaofei Yuan
- College
of Science and Engineering, Division of Biomedical Engineering, School
of Engineering, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Jillian M. Couto
- College
of Science and Engineering, Division of Infrastructure and Environment,
School of Engineering, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Andrew Glidle
- College
of Science and Engineering, Division of Biomedical Engineering, School
of Engineering, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Yanqing Song
- College
of Science and Engineering, Division of Biomedical Engineering, School
of Engineering, University of Glasgow, Glasgow G12 8QQ, U.K
| | - William Sloan
- College
of Science and Engineering, Division of Infrastructure and Environment,
School of Engineering, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Huabing Yin
- College
of Science and Engineering, Division of Biomedical Engineering, School
of Engineering, University of Glasgow, Glasgow G12 8QQ, U.K
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12
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Yan XF, Xin L, Yen JT, Zeng Y, Jin S, Cheang QW, Fong RACY, Chiam KH, Liang ZX, Gao YG. Structural analyses unravel the molecular mechanism of cyclic di-GMP regulation of bacterial chemotaxis via a PilZ adaptor protein. J Biol Chem 2017; 293:100-111. [PMID: 29146598 DOI: 10.1074/jbc.m117.815704] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/10/2017] [Indexed: 01/09/2023] Open
Abstract
The bacterial second messenger cyclic di-GMP (c-di-GMP) has emerged as a prominent mediator of bacterial physiology, motility, and pathogenicity. c-di-GMP often regulates the function of its protein targets through a unique mechanism that involves a discrete PilZ adaptor protein. However, the molecular mechanism for PilZ protein-mediated protein regulation is unclear. Here, we present the structure of the PilZ adaptor protein MapZ cocrystallized in complex with c-di-GMP and its protein target CheR1, a chemotaxis-regulating methyltransferase in Pseudomonas aeruginosa This cocrystal structure, together with the structure of free CheR1, revealed that the binding of c-di-GMP induces dramatic structural changes in MapZ that are crucial for CheR1 binding. Importantly, we found that restructuring and repositioning of two C-terminal helices enable MapZ to disrupt the CheR1 active site by dislodging a structural domain. The crystallographic observations are reinforced by protein-protein binding and single cell-based flagellar motor switching analyses. Our studies further suggest that the regulation of chemotaxis by c-di-GMP through MapZ orthologs/homologs is widespread in proteobacteria and that the use of allosterically regulated C-terminal motifs could be a common mechanism for PilZ adaptor proteins. Together, the findings provide detailed structural insights into how c-di-GMP controls the activity of an enzyme target indirectly through a PilZ adaptor protein.
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Affiliation(s)
- Xin-Fu Yan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 639798, Singapore
| | - Lingyi Xin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jackie Tan Yen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 639798, Singapore
| | - Yukai Zeng
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, Number 07-01, S138671 Singapore, Singapore
| | - Shengyang Jin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 639798, Singapore
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | | | - Keng-Hwee Chiam
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, Number 07-01, S138671 Singapore, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 639798, Singapore; Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Singapore 138673, Singapore.
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13
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Co AD, Lagomarsino MC, Caselle M, Osella M. Stochastic timing in gene expression for simple regulatory strategies. Nucleic Acids Res 2017; 45:1069-1078. [PMID: 28180313 PMCID: PMC5388427 DOI: 10.1093/nar/gkw1235] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/09/2016] [Accepted: 11/24/2016] [Indexed: 12/15/2022] Open
Abstract
Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to reach in a precise time a threshold level of expression that triggers a specific downstream process. However, gene expression is subject to stochastic fluctuations, naturally inducing an uncertainty in this threshold-crossing time with potential consequences on biological functions and phenotypes. Here, we consider such ‘timing fluctuations’ and we ask how they can be controlled. Our analytical estimates and simulations show that, for an induced gene, timing variability is minimal if the threshold level of expression is approximately half of the steady-state level. Timing fluctuations can be reduced by increasing the transcription rate, while they are insensitive to the translation rate. In presence of self-regulatory strategies, we show that self-repression reduces timing noise for threshold levels that have to be reached quickly, while self-activation is optimal at long times. These results lay a framework for understanding stochasticity of endogenous systems such as the cell cycle, as well as for the design of synthetic trigger circuits.
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Affiliation(s)
- Alma Dal Co
- Department of Physics and INFN, Università degli Studi di Torino, via P. Giuria 1, Turin, Italy
| | - Marco Cosentino Lagomarsino
- Sorbonne Universités, Université Pierre et Marie Curie, Institut de Biologie Paris Seine, Place Jussieu 4, Paris, France.,UMR 7238 CNRS, Computational and Quantitative Biology, Paris, France.,IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, Milan, Italy
| | - Michele Caselle
- Department of Physics and INFN, Università degli Studi di Torino, via P. Giuria 1, Turin, Italy
| | - Matteo Osella
- Department of Physics and INFN, Università degli Studi di Torino, via P. Giuria 1, Turin, Italy
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14
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Sheats J, Sclavi B, Cosentino Lagomarsino M, Cicuta P, Dorfman KD. Role of growth rate on the orientational alignment of Escherichia coli in a slit. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170463. [PMID: 28680690 PMCID: PMC5493932 DOI: 10.1098/rsos.170463] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/19/2017] [Indexed: 05/08/2023]
Abstract
We present experimental data on the nematic alignment of Escherichia coli bacteria confined in a slit, with an emphasis on the effect of growth rate and corresponding changes in cell aspect ratio. Global alignment with the channel walls arises from the combination of local nematic ordering of nearby cells, induced by cell division and the elongated shape of the cells, and the preferential orientation of cells proximate to the side walls of the slit. Decreasing the growth rate leads to a decrease in alignment with the walls, which is attributed primarily to effects of changing cell aspect ratio rather than changes in the variance in cell area. Decreasing confinement also reduces the degree of alignment by a similar amount as a decrease in the growth rate, but the distribution of the degree of alignment differs. The onset of alignment with the channel walls is coincident with the slits reaching their steady-state occupancy and connected to the re-orientation of locally aligned regions with respect to the walls during density fluctuations.
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Affiliation(s)
- Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - Bianca Sclavi
- LBPA, UMR 8113 du CNRS, École Normale Supérieure de Cachan, Cachan, France
| | - Marco Cosentino Lagomarsino
- Sorbonne Universités, Université Pierre et Marie Curie, 4 Place Jussieu, Paris, France
- CNRS, UMR7238 Computational and Quantitative Biology, Paris, France
- IFOM Institute for Molecular Oncology, Milan, Italy
| | - Pietro Cicuta
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455, USA
- Author for correspondence: Kevin D. Dorfman e-mail:
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15
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Xu L, Xin L, Zeng Y, Yam JKH, Ding Y, Venkataramani P, Cheang QW, Yang X, Tang X, Zhang LH, Chiam KH, Yang L, Liang ZX. A cyclic di-GMP-binding adaptor protein interacts with a chemotaxis methyltransferase to control flagellar motor switching. Sci Signal 2016; 9:ra102. [PMID: 27811183 DOI: 10.1126/scisignal.aaf7584] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The bacterial messenger cyclic diguanylate monophosphate (c-di-GMP) binds to various effectors, the most common of which are single-domain PilZ proteins. These c-di-GMP effectors control various cellular functions and multicellular behaviors at the transcriptional or posttranslational level. We found that MapZ (methyltransferase-associated PilZ; formerly known as PA4608), a single-domain PilZ protein from the opportunistic pathogen Pseudomonas aeruginosa, directly interacted with the methyltransferase CheR1 and that this interaction was enhanced by c-di-GMP. In vitro assays indicated that, in the presence of c-di-GMP, MapZ inhibited CheR1 from methylating the chemoreceptor PctA, which would be expected to increase its affinity for chemoattractants and promote chemotaxis. MapZ localized to the poles of P. aeruginosa cells, where the flagellar motor and other chemotactic proteins, including PctA and CheR1, are also located. P. aeruginosa cells exhibit a random walk behavior by frequently switching the direction of flagellar rotation in a uniform solution. We showed that binding of c-di-GMP to MapZ decreased the frequency of flagellar motor switching and that MapZ was essential for generating the heterogeneous motility typical of P. aeruginosa cell populations and for efficient surface attachment during biofilm formation. Collectively, the studies revealed that c-di-GMP affects flagellar motor output by regulating the methylation of chemoreceptors through a single-domain PilZ adaptor protein.
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Affiliation(s)
- Linghui Xu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Lingyi Xin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yukai Zeng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Singapore 138671, Singapore
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551, Singapore
| | - Yichen Ding
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551, Singapore
| | - Prabhadevi Venkataramani
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Xiaobei Yang
- Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Xuhua Tang
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Lian-Hui Zhang
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
| | - Keng-Hwee Chiam
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Singapore 138671, Singapore
| | - Liang Yang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore. .,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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