1
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Recalde A, Abdul-Nabi J, Junker P, van der Does C, Elsässer J, van Wolferen M, Albers SV. The use of thermostable fluorescent proteins for live imaging in Sulfolobus acidocaldarius. Front Microbiol 2024; 15:1445186. [PMID: 39314874 PMCID: PMC11416942 DOI: 10.3389/fmicb.2024.1445186] [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: 06/06/2024] [Accepted: 08/19/2024] [Indexed: 09/25/2024] Open
Abstract
Introduction Among hyperthermophilic organisms, in vivo protein localization is challenging due to the high growth temperatures that can disrupt proper folding and function of mostly mesophilic-derived fluorescent proteins. While protein localization in the thermophilic model archaeon S. acidocaldarius has been achieved using antibodies with fluorescent probes in fixed cells, the use of thermostable fluorescent proteins for live imaging in thermophilic archaea has so far been unsuccessful. Given the significance of live protein localization in the field of archaeal cell biology, we aimed to identify fluorescent proteins for use in S. acidocaldarius. Methods We expressed various previously published and optimized thermostable fluorescent proteins along with fusion proteins of interest and analyzed the cells using flow cytometry and (thermo-) fluorescent microscopy. Results Of the tested proteins, thermal green protein (TGP) exhibited the brightest fluorescence when expressed in Sulfolobus cells. By optimizing the linker between TGP and a protein of interest, we could additionally successfully fuse proteins with minimal loss of fluorescence. TGP-CdvB and TGP-PCNA1 fusions displayed localization patterns consistent with previous immunolocalization experiments. Discussion These initial results in live protein localization in S. acidocaldarius at high temperatures, combined with recent advancements in thermomicroscopy, open new avenues in the field of archaeal cell biology. This progress finally enables localization experiments in thermophilic archaea, which have so far been limited to mesophilic organisms.
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Affiliation(s)
| | | | | | | | | | | | - Sonja-Verena Albers
- Molecular Biology of Archaea, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
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2
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Delgadillo-Guevara M, Halte M, Erhardt M, Popp PF. Fluorescent tools for the standardized work in Gram-negative bacteria. J Biol Eng 2024; 18:25. [PMID: 38589953 PMCID: PMC11003136 DOI: 10.1186/s13036-024-00420-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Standardized and thoroughly characterized genetic tools are a prerequisite for studying cellular processes to ensure the reusability and consistency of experimental results. The discovery of fluorescent proteins (FPs) represents a milestone in the development of genetic reporters for monitoring transcription or protein localization in vivo. FPs have revolutionized our understanding of cellular dynamics by enabling the real-time visualization and tracking of biological processes. Despite these advancements, challenges remain in the appropriate use of FPs, specifically regarding their proper application, protein turnover dynamics, and the undesired disruption of cellular functions. Here, we systematically compared a comprehensive set of 15 FPs and assessed their performance in vivo by focusing on key parameters, such as signal over background ratios and protein stability rates, using the Gram-negative model organism Salmonella enterica as a representative host. We evaluated four protein degradation tags in both plasmid- and genome-based systems and our findings highlight the necessity of introducing degradation tags to analyze time-sensitive cellular processes. We demonstrate that the gain of dynamics mediated by the addition of degradation tags impacts the cell-to-cell heterogeneity of plasmid-based but not genome-based reporters. Finally, we probe the applicability of FPs for protein localization studies in living cells using standard and super-resolution fluorescence microscopy. In summary, our study underscores the importance of careful FP selection and paves the way for the development of improved genetic reporters to enhance the reproducibility and reliability of fluorescence-based research in Gram-negative bacteria and beyond.
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Affiliation(s)
- Mario Delgadillo-Guevara
- Institute of Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Manuel Halte
- Institute of Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Marc Erhardt
- Institute of Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
- Max Planck Unit for the Science of Pathogens, Berlin, 10117, Germany
| | - Philipp F Popp
- Institute of Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany.
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3
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Hernandez-Beltran JCR, Rodríguez-Beltrán J, Aguilar-Luviano OB, Velez-Santiago J, Mondragón-Palomino O, MacLean RC, Fuentes-Hernández A, San Millán A, Peña-Miller R. Plasmid-mediated phenotypic noise leads to transient antibiotic resistance in bacteria. Nat Commun 2024; 15:2610. [PMID: 38521779 PMCID: PMC10960800 DOI: 10.1038/s41467-024-45045-0] [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: 04/24/2023] [Accepted: 01/12/2024] [Indexed: 03/25/2024] Open
Abstract
The rise of antibiotic resistance is a critical public health concern, requiring an understanding of mechanisms that enable bacteria to tolerate antimicrobial agents. Bacteria use diverse strategies, including the amplification of drug-resistance genes. In this paper, we showed that multicopy plasmids, often carrying antibiotic resistance genes in clinical bacteria, can rapidly amplify genes, leading to plasmid-mediated phenotypic noise and transient antibiotic resistance. By combining stochastic simulations of a computational model with high-throughput single-cell measurements of blaTEM-1 expression in Escherichia coli MG1655, we showed that plasmid copy number variability stably maintains populations composed of cells with both low and high plasmid copy numbers. This diversity in plasmid copy number enhances the probability of bacterial survival in the presence of antibiotics, while also rapidly reducing the burden of carrying multiple plasmids in drug-free environments. Our results further support the tenet that multicopy plasmids not only act as vehicles for the horizontal transfer of genetic information between cells but also as drivers of bacterial adaptation, enabling rapid modulation of gene copy numbers. Understanding the role of multicopy plasmids in antibiotic resistance is critical, and our study provides insights into how bacteria can transiently survive lethal concentrations of antibiotics.
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Affiliation(s)
- J Carlos R Hernandez-Beltran
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, 62210, Cuernavaca, México.
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
| | | | | | - Jesús Velez-Santiago
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, 62210, Cuernavaca, México
| | - Octavio Mondragón-Palomino
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - R Craig MacLean
- Department of Biology, University of Oxford, OX1 3SZ, Oxford, UK
| | - Ayari Fuentes-Hernández
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, 62210, Cuernavaca, México
| | - Alvaro San Millán
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología - CSIC, 28049, Madrid, Spain
| | - Rafael Peña-Miller
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, 62210, Cuernavaca, México.
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4
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Song D, Chen X, Yao H, Kong G, Xu M, Guo J, Sun G. The variations of native plasmids greatly affect the cell surface hydrophobicity of sphingomonads. mSystems 2023; 8:e0086223. [PMID: 37909742 PMCID: PMC10734547 DOI: 10.1128/msystems.00862-23] [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: 08/16/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Microbial cell surface hydrophobicity (CSH) reflects nonspecific adhesion ability and affects various physiological processes, such as biofilm formation and pollutant biodegradation. Understanding the regulation mechanisms of CSH will contribute to illuminating microbial adaptation strategies and provide guidance for controlling CSH artificially to benefit humans. Sphingomonads, a common bacterial group with great xenobiotic-degrading ability, generally show higher CSH than typical Gram-negative bacteria, which plays a positive role in organic pollutant capture and cell colonization. This study verified that the variations of two native plasmids involved in synthesizing outer membrane proteins and polysaccharides greatly affected the CSH of sphingomonads. It is feasible to control their CSH by changing the plasmid copy number and sequences. Additionally, considering that plasmids are likely to evolve faster than chromosomes, the CSH of sphingomonads may evolve quickly to respond to environmental changes. Our results provide valuable insights into the CSH regulation and evolution of sphingomonads.
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Affiliation(s)
- Da Song
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Xingjuan Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Hui Yao
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Guannan Kong
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
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5
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Dewan I, Uecker H. A mathematician's guide to plasmids: an introduction to plasmid biology for modellers. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001362. [PMID: 37505810 PMCID: PMC10433428 DOI: 10.1099/mic.0.001362] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023]
Abstract
Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.
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Affiliation(s)
- Ian Dewan
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hildegard Uecker
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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6
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Singh B, Kumar A, Saini AK, Saini RV, Thakur R, Mohammed SA, Tuli HS, Gupta VK, Areeshi MY, Faidah H, Jalal NA, Haque S. Strengthening microbial cell factories for efficient production of bioactive molecules. Biotechnol Genet Eng Rev 2023:1-34. [PMID: 36809927 DOI: 10.1080/02648725.2023.2177039] [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: 08/11/2022] [Accepted: 01/21/2023] [Indexed: 02/24/2023]
Abstract
High demand of bioactive molecules (food additives, antibiotics, plant growth enhancers, cosmetics, pigments and other commercial products) is the prime need for the betterment of human life where the applicability of the synthetic chemical product is on the saturation due to associated toxicity and ornamentations. It has been noticed that the discovery and productivity of such molecules in natural scenarios are limited due to low cellular yields as well as less optimized conventional methods. In this respect, microbial cell factories timely fulfilling the requirement of synthesizing bioactive molecules by improving production yield and screening more promising structural homologues of the native molecule. Where the robustness of the microbial host can be potentially achieved by taking advantage of cell engineering approaches such as tuning functional and adjustable factors, metabolic balancing, adapting cellular transcription machinery, applying high throughput OMICs tools, stability of genotype/phenotype, organelle optimizations, genome editing (CRISPER/Cas mediated system) and also by developing accurate model systems via machine-learning tools. In this article, we provide an overview from traditional to recent trends and the application of newly developed technologies, for strengthening the systemic approaches and providing future directions for enhancing the robustness of microbial cell factories to speed up the production of biomolecules for commercial purposes.
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Affiliation(s)
- Bharat Singh
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Ankit Kumar
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gurugram, India
| | - Adesh Kumar Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Reena Vohra Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Rahul Thakur
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Shakeel A Mohammed
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Hardeep Singh Tuli
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland's Rural College (SRUC), Edinburgh, UK
| | - Mohammed Y Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Hani Faidah
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
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7
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The Sixth Element: a 102-kb RepABC Plasmid of Xenologous Origin Modulates Chromosomal Gene Expression in Dinoroseobacter shibae. mSystems 2022; 7:e0026422. [PMID: 35920548 PMCID: PMC9426580 DOI: 10.1128/msystems.00264-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The model organism Dinoroseobacter shibae and many other marine Rhodobacterales (Roseobacteraceae, Alphaproteobacteria) are characterized by a multipartite genome organization. Here, we show that the original isolate (Dshi-6) contained six extrachromosomal replicons (ECRs), whereas the strain deposited at the DSMZ (Dshi-5) lacked a 102-kb plasmid. To determine the role of the sixth plasmid, we investigated the genomic and physiological differences between the two strains. Therefore, both genomes were (re)sequenced, and gene expression, growth, and substrate utilization were examined. For comparison, we included additional plasmid-cured strains in the analysis. In the Dshi-6 population, the conjugative 102-kb RepABC-9 plasmid was present in only about 50% of the cells, irrespective of its experimentally validated stability. In the presence of the sixth plasmid, copy number changes of other ECRs, in particular, a decrease of the 86-kb plasmid, were observed. The most conspicuous finding was the strong influence of plasmids on chromosomal gene expression, especially the repression of the CtrA regulon and the activation of the denitrification gene cluster. Expression is inversely controlled by either the presence of the 102-kb plasmid or the absence of the 86-kb plasmid. We identified regulatory genes on both plasmids, i.e., a sigma 70 factor and a quorum sensing synthase, that might be responsible for these major changes. The tremendous effects that were probably even underestimated challenge the current understanding of the relevance of volatile plasmids not only for the original host but also for new recipients after conjugation. IMPORTANCE Plasmids are small DNA molecules that replicate independently of the bacterial chromosome. The common view of the role of plasmids is dominated by the accumulation of resistance genes, which is responsible for the antibiotic crisis in health care and livestock breeding. Beyond rapid adaptations to a changing environment, no general relevance for the host cell’s regulome was attributed to these volatile ECRs. The current study shows for the model organism D. shibae that its chromosomal gene expression is strongly influenced by two plasmids. We provide evidence that the gain or loss of plasmids not only results in minor alterations of the genetic repertoire but also can have tremendous effects on bacterial physiology. The central role of some plasmids in the regulatory network of the host could also explain their persistence despite fitness costs, which has been described as the “plasmid paradox.”
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8
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Sassi AS, Garcia-Alcala M, Aldana M, Tu Y. Protein concentration fluctuations in the high expression regime: Taylor's law and its mechanistic origin. PHYSICAL REVIEW. X 2022; 12:011051. [PMID: 35756903 PMCID: PMC9233241 DOI: 10.1103/physrevx.12.011051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Protein concentration in a living cell fluctuates over time due to noise in growth and division processes. In the high expression regime, variance of the protein concentration in a cell was found to scale with the square of the mean, which belongs to a general phenomenon called Taylor's law (TL). To understand the origin for these fluctuations, we measured protein concentration dynamics in single E. coli cells from a set of strains with a variable expression of fluorescent proteins. The protein expression is controlled by a set of constitutive promoters with different strength, which allows to change the expression level over 2 orders of magnitude without introducing noise from fluctuations in transcription regulators. Our data confirms the square TL, but the prefactor A has a cell-to-cell variation independent of the promoter strength. Distributions of the normalized protein concentration for different promoters are found to collapse onto the same curve. To explain these observations, we used a minimal mechanistic model to describe the stochastic growth and division processes in a single cell with a feedback mechanism for regulating cell division. In the high expression regime where extrinsic noise dominates, the model reproduces our experimental results quantitatively. By using a mean-field approximation in the minimal model, we showed that the stochastic dynamics of protein concentration is described by a Langevin equation with multiplicative noise. The Langevin equation has a scale invariance which is responsible for the square TL. By solving the Langevin equation, we obtained an analytical solution for the protein concentration distribution function that agrees with experiments. The solution shows explicitly how the prefactor A depends on strength of different noise sources, which explains its cell-to-cell variability. By using this approach to analyze our single-cell data, we found that the noise in production rate dominates the noise from cell division. The deviation from the square TL in the low expression regime can also be captured in our model by including intrinsic noise in the production rate.
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Affiliation(s)
| | - Mayra Garcia-Alcala
- Department of Molecular and Cellular Biology, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Maximino Aldana
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Yuhai Tu
- IBM T.J. Watson Research Center, Yorktown Heights, NY 10598, U.S.A
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9
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Gerhardt KP, Rao SD, Olson EJ, Igoshin OA, Tabor JJ. Independent control of mean and noise by convolution of gene expression distributions. Nat Commun 2021; 12:6957. [PMID: 34845228 PMCID: PMC8630168 DOI: 10.1038/s41467-021-27070-5] [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: 03/10/2021] [Accepted: 11/03/2021] [Indexed: 11/28/2022] Open
Abstract
Gene expression noise can reduce cellular fitness or facilitate processes such as alternative metabolism, antibiotic resistance, and differentiation. Unfortunately, efforts to study the impacts of noise have been hampered by a scaling relationship between noise and expression level from individual promoters. Here, we use theory to demonstrate that mean and noise can be controlled independently by expressing two copies of a gene from separate inducible promoters in the same cell. We engineer low and high noise inducible promoters to validate this result in Escherichia coli, and develop a model that predicts the experimental distributions. Finally, we use our method to reveal that the response of a promoter to a repressor is less sensitive with higher repressor noise and explain this result using a law from probability theory. Our approach can be applied to investigate the effects of noise on diverse biological pathways or program cellular heterogeneity for synthetic biology applications.
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Affiliation(s)
- Karl P Gerhardt
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Satyajit D Rao
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Evan J Olson
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
- Department of Biosciences, Rice University, 6100 Main Street, Houston, TX, 77005, USA
- Center for Theoretical Biophysics, Rice University, 6100 Main Street, Houston, TX, 77005, USA
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA.
- Department of Biosciences, Rice University, 6100 Main Street, Houston, TX, 77005, USA.
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10
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Round JW, Robeck LD, Eltis LD. An Integrative Toolbox for Synthetic Biology in Rhodococcus. ACS Synth Biol 2021; 10:2383-2395. [PMID: 34428025 DOI: 10.1021/acssynbio.1c00292] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of microbial cell factories requires robust synthetic biology tools to reduce design uncertainty and accelerate the design-build-test-learn process. Herein, we developed a suite of integrative genetic tools to facilitate the engineering of Rhodococcus, a genus of bacteria with considerable biocatalytic potential. We first created pRIME, a modular, copy-controlled integrative-vector, to provide a robust platform for strain engineering and characterizing genetic parts. This vector was then employed to benchmark a series of strong promoters. We found PM6 to be the strongest constitutive rhodococcal promoter, 2.5- to 3-fold stronger than the next in our study, while overall promoter activities ranged 23-fold between the weakest and strongest promoters during exponential growth. Next, we used an optimized variant of PM6 to develop hybrid-promoters and integrative vectors to allow for tetracycline-inducible gene expression in Rhodococcus. The best of the resulting hybrid-promoters maintained a maximal activity of ∼50% of PM6 and displayed an induction factor of ∼40-fold. Finally, we developed and implemented a uLoop-derived Golden Gate assembly strategy for high-throughput DNA assembly in Rhodococcus. To demonstrate the utility of our approaches, pRIME was used to engineer Rhodococcus jostii RHA1 to grow on vanillin at concentrations 10-fold higher than what the wild-type strain tolerated. Overall, this study provides a suite of tools that will accelerate the engineering of Rhodococcus for various biocatalytic applications, including the sustainable production of chemicals from lignin-derived aromatics.
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Affiliation(s)
- James W. Round
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Logan D. Robeck
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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11
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Glasscock CJ, Biggs BW, Lazar JT, Arnold JH, Burdette LA, Valdes A, Kang MK, Tullman-Ercek D, Tyo KEJ, Lucks JB. Dynamic Control of Gene Expression with Riboregulated Switchable Feedback Promoters. ACS Synth Biol 2021; 10:1199-1213. [PMID: 33834762 DOI: 10.1021/acssynbio.1c00015] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One major challenge in synthetic biology is the deleterious impacts of cellular stress caused by expression of heterologous pathways, sensors, and circuits. Feedback control and dynamic regulation are broadly proposed strategies to mitigate this cellular stress by optimizing gene expression levels temporally and in response to biological cues. While a variety of approaches for feedback implementation exist, they are often complex and cannot be easily manipulated. Here, we report a strategy that uses RNA transcriptional regulators to integrate additional layers of control over the output of natural and engineered feedback responsive circuits. Called riboregulated switchable feedback promoters (rSFPs), these gene expression cassettes can be modularly activated using multiple mechanisms, from manual induction to autonomous quorum sensing, allowing control over the timing, magnitude, and autonomy of expression. We develop rSFPs in Escherichia coli to regulate multiple feedback networks and apply them to control the output of two metabolic pathways. We envision that rSFPs will become a valuable tool for flexible and dynamic control of gene expression in metabolic engineering, biological therapeutic production, and many other applications.
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Affiliation(s)
- Cameron J. Glasscock
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 113 Ho Plaza, Ithaca, New York 14853, United States
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Bradley W. Biggs
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - John T. Lazar
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Jack H. Arnold
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Lisa A. Burdette
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Aliki Valdes
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Min-Kyoung Kang
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Danielle Tullman-Ercek
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Keith E. J. Tyo
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Julius B. Lucks
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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12
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Petch JE, Gurnani P, Yilmaz G, Mastrotto F, Alexander C, Heeb S, Cámara M, Mantovani G. Combining Inducible Lectin Expression and Magnetic Glyconanoparticles for the Selective Isolation of Bacteria from Mixed Populations. ACS APPLIED MATERIALS & INTERFACES 2021; 13:19230-19243. [PMID: 33852268 DOI: 10.1021/acsami.1c00907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The selective isolation of bacteria from mixed populations has been investigated in varied applications ranging from differential pathogen identification in medical diagnostics and food safety to the monitoring of microbial stress dynamics in industrial bioreactors. Selective isolation techniques are generally limited to the confinement of small populations in defined locations, may be unable to target specific bacteria, or rely on immunomagnetic separation, which is not universally applicable. In this proof-of-concept work, we describe a novel strategy combining inducible bacterial lectin expression with magnetic glyconanoparticles (MGNPs) as a platform technology to enable selective bacterial isolation from cocultures. An inducible mutant of the type 1 fimbriae, displaying the mannose-specific lectin FimH, was constructed in Escherichia coli allowing for "on-demand" glycan-binding protein presentation following external chemical stimulation. Binding to glycopolymers was only observed upon fimbrial induction and was specific for mannosylated materials. A library of MGNPs was produced via the grafting of well-defined catechol-terminal glycopolymers prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization to magnetic nanoparticles. Thermal analysis revealed high functionalization (≥85% polymer by weight). Delivery of MGNPs to cocultures of fluorescently labeled bacteria followed by magnetic extraction resulted in efficient depletion of type 1 fimbriated target cells from wild-type or afimbriate E. coli. Extraction efficiency was found to be dependent on the molecular weight of the glycopolymers utilized to engineer the nanoparticles, with MGNPs decorated with shorter Dopa-(ManAA)50 mannosylated glycopolymers found to perform better than those assembled from a longer Dopa-(ManAA)200 analogue. The extraction efficiency of fimbriated E. coli was also improved when the counterpart strain did not harbor the genetic apparatus for the expression of the type 1 fimbriae. Overall, this work suggests that the modulation of the genetic apparatus encoding bacterial surface-associated lectins coupled with capture through MGNPs could be a versatile tool for the extraction of bacteria from mixed populations.
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Affiliation(s)
- Joshua E Petch
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
- Nottingham University Biodiscovery Institute, National Biofilms Innovation Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Pratik Gurnani
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Gokhan Yilmaz
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Francesca Mastrotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Cameron Alexander
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Stephan Heeb
- Nottingham University Biodiscovery Institute, National Biofilms Innovation Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Miguel Cámara
- Nottingham University Biodiscovery Institute, National Biofilms Innovation Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Giuseppe Mantovani
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
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13
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Beyond horizontal gene transfer: the role of plasmids in bacterial evolution. Nat Rev Microbiol 2021; 19:347-359. [PMID: 33469168 DOI: 10.1038/s41579-020-00497-1] [Citation(s) in RCA: 180] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2020] [Indexed: 12/27/2022]
Abstract
Plasmids have a key role in bacterial ecology and evolution because they mobilize accessory genes by horizontal gene transfer. However, recent studies have revealed that the evolutionary impact of plasmids goes above and beyond their being mere gene delivery platforms. Plasmids are usually kept at multiple copies per cell, producing islands of polyploidy in the bacterial genome. As a consequence, the evolution of plasmid-encoded genes is governed by a set of rules different from those affecting chromosomal genes, and these rules are shaped by unusual concepts in bacterial genetics, such as genetic dominance, heteroplasmy or segregational drift. In this Review, we discuss recent advances that underscore the importance of plasmids in bacterial ecology and evolution beyond horizontal gene transfer. We focus on new evidence that suggests that plasmids might accelerate bacterial evolution, mainly by promoting the evolution of plasmid-encoded genes, but also by enhancing the adaptation of their host chromosome. Finally, we integrate the most relevant theoretical and empirical studies providing a global understanding of the forces that govern plasmid-mediated evolution in bacteria.
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14
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Carruthers DN, Saleski TE, Scholz SA, Lin XN. Random Chromosomal Integration and Screening Yields E. coli K-12 Derivatives Capable of Efficient Sucrose Utilization. ACS Synth Biol 2020; 9:3311-3321. [PMID: 33236893 DOI: 10.1021/acssynbio.0c00392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Chromosomal expression of heterologous genes offers stability and maintenance advantages over episomal expression, yet remains difficult to optimize through site-specific integration. The challenge has in large part been due to the variability of chromosomal gene expression, which has only recently been shown to be affected by multiple factors, including the local genomic context. In this work we utilize Tn5 transposase to randomly integrate a three-gene csc operon encoding nonphosphotransferase sucrose catabolism into the E. coli K-12 chromosome. Isolates from the transposon library yielded a range of growth rates on sucrose as the sole carbon source, including some that were comparable to that of E. coli K-12 on glucose (μmax = 0.70 ± 0.03 h-1). Narrowness of the growth rate distributions and faster growth compared to plasmids indicate that efficient csc expression is attainable. Furthermore, enhanced growth rate upon transduction into strains that underwent adaptive laboratory evolution indicate that sucrose catabolism is not limiting to cellular growth. We also show that transduction of a csc fast-growth locus into an isobutanol production strain yields high titer (7.56 ± 0.25 g/L) on sucrose as the sole carbon source. Our results demonstrate that random integration is an effective strategy for optimizing heterologous expression within the context of cellular metabolism for both fast growth and biochemical production phenotypes.
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Affiliation(s)
- David N. Carruthers
- Chemical Engineering Department, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tatyana E. Saleski
- Chemical Engineering Department, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Scott A. Scholz
- Department of Biochemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Xiaoxia Nina Lin
- Chemical Engineering Department, University of Michigan, Ann Arbor, Michigan 48109, United States
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15
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Sánchez-Romero MA, Mérida-Floriano Á, Casadesús J. Copy Number Heterogeneity in the Virulence Plasmid of Salmonella enterica. Front Microbiol 2020; 11:599931. [PMID: 33343541 PMCID: PMC7746676 DOI: 10.3389/fmicb.2020.599931] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
Quantitative PCR analysis shows that the virulence plasmid of Salmonella enterica serovar Typhimurium (pSLT) is a low-copy-number plasmid, with 1–2 copies per chromosome. However, fluorescence microscopy observation of pSLT labeled with a lacO fluorescent tag reveals cell-to-cell differences in the number of foci, which ranges from 1 to 8. As each focus must correspond to ≥1 plasmid copy, the number of foci can be expected to indicate the minimal number of pSLT copies per cell. A correlation is found between the number of foci and the bacterial cell volume. In contrast, heterogeneity in the number of foci appears to be independent of the cell volume and may have stochastic origin. As a consequence of copy number heterogeneity, expression of a pSLT-bone reporter gene shows high levels of cell-to-cell variation, especially in actively dividing cultures. These observations support the notion that low-copy-number plasmids can be a source of gene expression noise in bacterial populations.
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Affiliation(s)
| | | | - Josep Casadesús
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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16
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An agent-based lattice model for the emergence of anti-microbial resistance. J Theor Biol 2020; 486:110080. [DOI: 10.1016/j.jtbi.2019.110080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 11/19/2022]
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17
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Losoi PS, Santala VP, Santala SM. Enhanced Population Control in a Synthetic Bacterial Consortium by Interconnected Carbon Cross-Feeding. ACS Synth Biol 2019; 8:2642-2650. [PMID: 31751122 DOI: 10.1021/acssynbio.9b00316] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Engineered microbial consortia can provide several advantages over monocultures in terms of utilization of mixed substrates, resistance to perturbations, and division of labor in complex tasks. However, maintaining stability, reproducibility, and control over population levels in variable conditions can be challenging in multispecies cultures. In our study, we modeled and constructed a synthetic symbiotic consortium with a genetically encoded carbon cross-feeding system. The system is based on strains of Escherichia coli and Acinetobacter baylyi ADP1, both engineered to be incapable of growing on glucose on their own. In a culture supplemented with glucose as the sole carbon source, growth of the two strains is afforded by the exchange of gluconate and acetate, resulting in inherent control over carbon availability and population balance. We investigated the system robustness in terms of stability and population control under different inoculation ratios, substrate concentrations, and cultivation scales, both experimentally and by modeling. To illustrate how the system might facilitate division of genetic circuits among synthetic microbial consortia, a green fluorescent protein sensitive to pH and a slowly maturing red fluorescent protein were expressed in the consortium as measures of a circuit's susceptibility to external and internal variability, respectively. The symbiotic consortium maintained stable and linear growth and circuit performance regardless of the initial substrate concentration or inoculation ratio. The developed cross-feeding system provides simple and reliable means for population control without expression of non-native elements or external inducer addition, being potentially exploitable in consortia applications involving precisely defined cell tasks or division of labor.
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Affiliation(s)
- Pauli S. Losoi
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta campus, Korkeakoulunkatu 8, Tampere, 33720, Finland
| | - Ville P. Santala
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta campus, Korkeakoulunkatu 8, Tampere, 33720, Finland
| | - Suvi M. Santala
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta campus, Korkeakoulunkatu 8, Tampere, 33720, Finland
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18
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Menn D, Sochor P, Goetz H, Tian XJ, Wang X. Intracellular Noise Level Determines Ratio Control Strategy Confined by Speed-Accuracy Trade-off. ACS Synth Biol 2019; 8:1352-1360. [PMID: 31083890 DOI: 10.1021/acssynbio.9b00030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Robust and precise ratio control of heterogeneous phenotypes within an isogenic population is an essential task, especially in the development and differentiation of a large number of cells such as bacteria, sensory receptors, and blood cells. However, the mechanisms of such ratio control are poorly understood. Here, we employ experimental and mathematical techniques to understand the combined effects of signal induction and gene expression stochasticity on phenotypic multimodality. We identify two strategies to control phenotypic ratios from an initially homogeneous population, suitable roughly to high-noise and low-noise intracellular environments, and we show that both can be used to generate precise fractional differentiation. In noisy gene expression contexts, such as those found in bacteria, induction within the circuit's bistable region is enough to cause noise-induced bimodality within a feasible time frame. However, in less noisy contexts, such as tightly controlled eukaryotic systems, spontaneous state transitions are rare and hence bimodality needs to be induced with a controlled pulse of induction that falls outside the bistable region. Finally, we show that noise levels, system response time, and ratio tuning accuracy impose trade-offs and limitations on both ratio control strategies, which guide the selection of strategy alternatives.
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Affiliation(s)
- David Menn
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
| | - Patrick Sochor
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
| | - Hanah Goetz
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
| | - Xiao-Jun Tian
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
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19
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Hsu TM, Chang YR. High-Copy-Number Plasmid Segregation-Single-Molecule Dynamics in Single Cells. Biophys J 2019; 116:772-780. [PMID: 30773297 DOI: 10.1016/j.bpj.2019.01.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 12/21/2022] Open
Abstract
Bacterial high-copy-number (hcn) plasmids provide an excellent model to study the underlying physical mechanisms of DNA segment segregation in an intracellular context. Using two-color fluorescent repressor-operator systems and a synthetic repressible replication origin, we tracked the motion and segregation of single hcn plasmid molecules in individual cells. The plasmid diffusion dynamics revealed between-plasmid temporal associations (clustering) as well as entropic and elastic recoiling forces in the confined intracellular spaces outside of nucleoids. These two effects could be effectively used in models to predict the heterogeneity of segregation. Additionally, the motile behaviors of hcn plasmids provide quantitative estimates of entropic exclusion strength and dynamic associations between DNA segments. Overall, this study utilizes a, to our knowledge, novel approach to predict the polymer dynamics of DNA segments in spatially confined, crowded cellular compartments as well as during bacterial chromosome segregation.
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Affiliation(s)
- Tai-Ming Hsu
- Department of Physics, National Taiwan Normal University, Taipei, Taiwan
| | - Yi-Ren Chang
- Department of Physics, National Taiwan Normal University, Taipei, Taiwan.
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20
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Engineered promoters enable constant gene expression at any copy number in bacteria. Nat Biotechnol 2018; 36:352-358. [PMID: 29553576 DOI: 10.1038/nbt.4111] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/23/2018] [Indexed: 11/09/2022]
Abstract
The internal environment of growing cells is variable and dynamic, making it difficult to introduce reliable parts, such as promoters, for genetic engineering. Here, we applied control-theoretic ideas to design promoters that maintained constant levels of expression at any copy number. Theory predicts that independence to copy number can be achieved by using an incoherent feedforward loop (iFFL) if the negative regulation is perfectly non-cooperative. We engineered iFFLs into Escherichia coli promoters using transcription-activator-like effectors (TALEs). These promoters had near-identical expression in different genome locations and plasmids, even when their copy number was perturbed by genomic mutations or changes in growth medium composition. We applied the stabilized promoters to show that a three-gene metabolic pathway to produce deoxychromoviridans could retain function without re-tuning when the stabilized-promoter-driven genes were moved from a plasmid into the genome.
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21
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Song Y, Nikoloff JM, Fu G, Chen J, Li Q, Xie N, Zheng P, Sun J, Zhang D. Promoter Screening from Bacillus subtilis in Various Conditions Hunting for Synthetic Biology and Industrial Applications. PLoS One 2016; 11:e0158447. [PMID: 27380260 PMCID: PMC4933340 DOI: 10.1371/journal.pone.0158447] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 06/16/2016] [Indexed: 11/24/2022] Open
Abstract
The use of Bacillus subtilis in synthetic biology and metabolic engineering is highly desirable to take advantage of the unique metabolic pathways present in this organism. To do this, an evaluation of B. subtilis’ intrinsic biological parts is required to determine the best strategies to accurately regulate metabolic circuits and expression of target proteins. The strengths of promoter candidates were evaluated by measuring relative fluorescence units of a green fluorescent protein reporter, integrated into B. subtilis’ chromosome. A total of 84 predicted promoter sequences located upstream of different classes of proteins including heat shock proteins, cell-envelope proteins, and proteins resistant against toxic metals (based on similarity) and other kinds of genes were tested. The expression levels measured ranged from 0.0023 to 4.53-fold of the activity of the well-characterized strong promoter P43. No significant shifts were observed when strains, carrying different promoter candidates, were cultured at high temperature or in media with ethanol, but some strains showed increased activity when cultured under high osmotic pressure. Randomly selected promoter candidates were tested and found to activate transcription of thermostable β-galactosidase (bgaB) at a similar level, implying the ability of these sequences to function as promoter elements in multiple genetic contexts. In addition, selected promoters elevated the final production of both cytoplasmic bgaB and secreted protein α-amylase to about fourfold and twofold, respectively. The generated data allows a deeper understanding of B. subtilis’ metabolism and will facilitate future work to develop this organism for synthetic biology.
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Affiliation(s)
- Yafeng Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jonas M Nikoloff
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Gang Fu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jingqi Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Qinggang Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Nengzhong Xie
- National Engineering Research Center for Non-food Biorefinery, State Key Laboratory of Non-food Biomass Energy and Enzyme Technology, Nanning 5300074, P. R. China
- Guangxi Biomass Industrialization Engineering Institute, Guangxi Academy of Sciences, Nanning 530007, P. R. China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
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22
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Koutsoumanis KP, Aspridou Z. Individual cell heterogeneity in Predictive Food Microbiology: Challenges in predicting a "noisy" world. Int J Food Microbiol 2016; 240:3-10. [PMID: 27412586 DOI: 10.1016/j.ijfoodmicro.2016.06.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/13/2016] [Accepted: 06/19/2016] [Indexed: 11/25/2022]
Abstract
Gene expression is a fundamentally noisy process giving rise to a significant cell to cell variability at the phenotype level. The phenotypic noise is manifested in a wide range of microbial traits. Heterogeneous behavior of individual cells is observed at the growth, survival and inactivation responses and should be taken into account in the context of Predictive Food Microbiology (PMF). Recent methodological advances can be employed for the study and modeling of single cell dynamics leading to a new generation of mechanistic models which can provide insight into the link between phenotype, gene-expression, protein and metabolic functional units at the single cell level. Such models however, need to deal with an enormous amount of interactions and processes that influence each other, forming an extremely complex system. In this review paper, we discuss the importance of noise and present the future challenges in predicting the "noisy" microbial responses in foods.
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Affiliation(s)
- Konstantinos P Koutsoumanis
- Laboratory of Food Microbiology and Hygiene, Department of Food Science and Technology, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
| | - Zafiro Aspridou
- Laboratory of Food Microbiology and Hygiene, Department of Food Science and Technology, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
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23
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Epidemiological and clinical features for cefepime heteroresistant Escherichia coli infections in Southwest China. Eur J Clin Microbiol Infect Dis 2016; 35:571-8. [PMID: 26815433 DOI: 10.1007/s10096-015-2572-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/30/2015] [Indexed: 01/13/2023]
Abstract
Phenotypic heteroresistance (PHR) is common in a weight of microbes and plays an important role in the evolution of antibiotic resistance. However, PHR to cefepime (FEP-PHR) among invasive Escherichia coli (E. coli) has not been reported. This study aimed to report the characteristics of invasive E. coli with FEP-PHR traits and further to investigate the predisposing factors for its acquisition. A retrospective case-control study was conducted in a teaching hospital in Southwest China. A total of 319 successive and non-duplicate E. coli strains were isolated from blood and other sterile body fluids between July 2011 and August 2013. Among the seventy (70/319, 21.9 %) isolates harboring FEP-PHR traits, 30 (42.9 %) isolates were isolated from blood, 14 (20.0 %) isolates were isolated from bile, and 13 (18.6 %) isolates were isolated from drainage. FEP-PHR isolates were verified by population analysis profile (PAP) assays. Male gender, receipt of total parenteral nutrition, cephalosporins exposure, and production of extended spectrum betalactamases (ESBL) were independent risk factors for the acquisition of invasive E. coli with FEP-PHR traits. Pulsedfield gel electrophoresis (PFGE) revealed clonal diversity among the FEP-PHR isolates. The prevalence of heteroresistance to cefepime among invasive E. coli isolates merits great attention and heteroresistance may lead to the emergence of resistance strains. Therefore, systematical analysis of risk factors, careful interpretation of antibiotic susceptibility results and appropriate prescription of therapeutic strategy could help to prevent misreporting and therapeutic failure.
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24
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Jahn M, Günther S, Müller S. Non-random distribution of macromolecules as driving forces for phenotypic variation. Curr Opin Microbiol 2015; 25:49-55. [DOI: 10.1016/j.mib.2015.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/04/2015] [Accepted: 04/21/2015] [Indexed: 12/19/2022]
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25
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Jahn M, Vorpahl C, Türkowsky D, Lindmeyer M, Bühler B, Harms H, Müller S. Accurate Determination of Plasmid Copy Number of Flow-Sorted Cells using Droplet Digital PCR. Anal Chem 2014; 86:5969-76. [DOI: 10.1021/ac501118v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Michael Jahn
- Helmholtz-Centre
for Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Carsten Vorpahl
- Helmholtz-Centre
for Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Dominique Türkowsky
- Helmholtz-Centre
for Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Martin Lindmeyer
- Laboratory
of Chemical Biotechnology, Department of Biochemical and Chemical
Engineering, TU Dortmund University, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Bruno Bühler
- Laboratory
of Chemical Biotechnology, Department of Biochemical and Chemical
Engineering, TU Dortmund University, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Hauke Harms
- Helmholtz-Centre
for Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Susann Müller
- Helmholtz-Centre
for Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
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26
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Brewster RC, Weinert FM, Garcia HG, Song D, Rydenfelt M, Phillips R. The transcription factor titration effect dictates level of gene expression. Cell 2014; 156:1312-1323. [PMID: 24612990 DOI: 10.1016/j.cell.2014.02.022] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 11/15/2013] [Accepted: 02/03/2014] [Indexed: 02/01/2023]
Abstract
Models of transcription are often built around a picture of RNA polymerase and transcription factors (TFs) acting on a single copy of a promoter. However, most TFs are shared between multiple genes with varying binding affinities. Beyond that, genes often exist at high copy number-in multiple identical copies on the chromosome or on plasmids or viral vectors with copy numbers in the hundreds. Using a thermodynamic model, we characterize the interplay between TF copy number and the demand for that TF. We demonstrate the parameter-free predictive power of this model as a function of the copy number of the TF and the number and affinities of the available specific binding sites; such predictive control is important for the understanding of transcription and the desire to quantitatively design the output of genetic circuits. Finally, we use these experiments to dynamically measure plasmid copy number through the cell cycle.
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Affiliation(s)
- Robert C Brewster
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Franz M Weinert
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Dan Song
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Biophysics Program, Harvard Medical School, Boston, MA 02115, USA
| | - Mattias Rydenfelt
- Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rob Phillips
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.
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27
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Williams K, Savageau MA, Blumenthal RM. A bistable hysteretic switch in an activator-repressor regulated restriction-modification system. Nucleic Acids Res 2013; 41:6045-57. [PMID: 23630319 PMCID: PMC3695507 DOI: 10.1093/nar/gkt324] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Restriction–modification (RM) systems are extremely widespread among bacteria and archaea, and are often specified by mobile genetic elements. In type II RM systems, where the restriction endonuclease (REase) and protective DNA methyltransferase (MTase) are separate proteins, a major regulatory challenge is delaying expression of the REase relative to the MTase after RM genes enter a new host cell. Basic understanding of this regulation is available for few RM systems, and detailed understanding for none. The PvuII RM system is one of a large subset in which the central regulatory role is played by an activator–repressor protein (called C, for controller). REase expression depends upon activation by C, whereas expression of the MTase does not. Thus delay of REase expression depends on the rate of C-protein accumulation. This is a nonlinear process, as C also activates transcription of its own gene. Mathematical modeling of the PvuII system led to the unexpected predictions of responsiveness to a factor not previously studied in RM system control—gene copy number—and of a hysteretic response. In this study, those predictions have been confirmed experimentally. The results may apply to many other C-regulated RM systems, and help explain their ability to spread so widely.
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Affiliation(s)
- Kristen Williams
- Department of Medical Microbiology & Immunology, and Program in Bioinformatics, University of Toledo, Toledo, OH 43614, USA
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Balzer S, Kucharova V, Megerle J, Lale R, Brautaset T, Valla S. A comparative analysis of the properties of regulated promoter systems commonly used for recombinant gene expression in Escherichia coli. Microb Cell Fact 2013; 12:26. [PMID: 23506076 PMCID: PMC3621392 DOI: 10.1186/1475-2859-12-26] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 03/01/2013] [Indexed: 11/20/2022] Open
Abstract
Background Production of recombinant proteins in bacteria for academic and commercial purposes is a well established field; however the outcomes of process developments for specific proteins are still often unpredictable. One reason is the limited understanding of the performance of expression cassettes relative to each other due to different genetic contexts. Here we report the results of a systematic study aiming at exclusively comparing commonly used regulator/promoter systems by standardizing the designs of the replicon backbones. Results The vectors used in this study are based on either the RK2- or the pMB1- origin of replication and contain the regulator/promoter regions of XylS/Pm (wild-type), XylS/Pm ML1-17 (a Pm variant), LacI/PT7lac, LacI/Ptrc and AraC/PBAD to control expression of different proteins with various origins. Generally and not unexpected high expression levels correlate with high replicon copy number and the LacI/PT7lac system generates more transcript than all the four other cassettes. However, this transcriptional feature does not always lead to a correspondingly more efficient protein production, particularly if protein functionality is considered. In most cases the XylS/Pm ML1-17 and LacI/PT7lac systems gave rise to the highest amounts of functional protein production, and the XylS/Pm ML1-17 is the most flexible in the sense that it does not require any specific features of the host. The AraC/PBAD system is very good with respect to tightness, and a commonly used bioinformatics prediction tool (RBS calculator) suggested that it has the most translation-efficient UTR. Expression was also studied by flow cytometry in individual cells, and the results indicate that cell to cell heterogeneity is very relevant for understanding protein production at the population level. Conclusions The choice of expression system needs to be evaluated for each specific case, but we believe that the standardized vectors developed for this study can be used to more easily identify the nature of case-specific bottlenecks. By then taking into account the relevant characteristics of each expression cassette it will be easier to make the best choice with respect to the goal of achieving high levels of protein expression in functional or non-functional form.
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Affiliation(s)
- Simone Balzer
- Department of Biotechnology, NTNU, Sem Sælands vei 6, Trondheim 7491, Norway
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Tal S, Paulsson J. Evaluating quantitative methods for measuring plasmid copy numbers in single cells. Plasmid 2012; 67:167-73. [PMID: 22305922 DOI: 10.1016/j.plasmid.2012.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 01/03/2012] [Accepted: 01/04/2012] [Indexed: 11/17/2022]
Abstract
The life of plasmids is a constant battle against fluctuations: failing to correct copy number fluctuations can increase the plasmid loss rate by many orders of magnitude, as can a failure to more evenly divide the copies between daughters at cell division. Plasmids are therefore long-standing model systems for stochastic processes in cells, much thanks to the efforts of Kurt Nordström to whose memory this issue is dedicated. Here we analyze a range of experimental methods for measuring plasmid copy numbers in single cells, focusing on challenges, trade-offs, and necessary experimental controls. In particular we analyze published and unpublished strategies to infer copy numbers from expression of plasmid-encoded reporters, direct labeling of plasmids with fluorescent probes or DNA binding proteins fused to fluorescent reporters, PCR based methods applied to single cell lysates, and plasmid-specific replication arrest. We conclude that no method currently exists to measure plasmid copy numbers in single cells, and that most methods are overwhelmed by various types of experimental noise. We also discuss how accurate methods can be developed.
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Affiliation(s)
- Shay Tal
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA
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El-Halfawy OM, Valvano MA. Heteroresistance of opportunistic bacteria to antimicrobial peptides: a new challenge to antimicrobial therapy of cystic fibrosis infections. ACTA ACUST UNITED AC 2011. [DOI: 10.2217/thy.11.69] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Ghozzi S, Wong Ng J, Chatenay D, Robert J. Inference of plasmid-copy-number mean and noise from single-cell gene expression data. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:051916. [PMID: 21230509 DOI: 10.1103/physreve.82.051916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 10/05/2010] [Indexed: 05/30/2023]
Abstract
Plasmids are extrachromosomal DNA molecules which code for their own replication. We previously reported a setup using genes coding for fluorescent proteins of two colors that allowed us, using a simple model, to extract the plasmid-copy-number noise in a monoclonal population of bacteria [J. Wong Ng, Phys. Rev. E 81, 011909 (2010)]. Here we present a detailed calculation relating this noise to the measured levels of fluorescence, taking into account all sources of fluorescence fluctuations: not only the fluctuation of gene expression as in the simple model but also the growth and division of bacteria, the nonuniform distribution of their ages, the random partition of proteins at divisions, and the replication and partition of plasmids and chromosome. We show how to use the chromosome as a reference, which helps extracting the plasmid-copy-number noise in a self-consistent manner.
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Affiliation(s)
- Stéphane Ghozzi
- Laboratoire de Physique Statistique, École Normale Supérieure, UPMC Univ Paris 06, Université Paris Diderot, CNRS, 24 rue Lhomond, 75005 Paris, France.
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