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Krajewska J, Tyski S, Laudy AE. In Vitro Resistance-Predicting Studies and In Vitro Resistance-Related Parameters-A Hit-to-Lead Perspective. Pharmaceuticals (Basel) 2024; 17:1068. [PMID: 39204172 PMCID: PMC11357384 DOI: 10.3390/ph17081068] [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: 07/26/2024] [Revised: 08/10/2024] [Accepted: 08/12/2024] [Indexed: 09/03/2024] Open
Abstract
Despite the urgent need for new antibiotics, very few innovative antibiotics have recently entered clinics or clinical trials. To provide a constant supply of new drug candidates optimized in terms of their potential to select for resistance in natural settings, in vitro resistance-predicting studies need to be improved and scaled up. In this review, the following in vitro parameters are presented: frequency of spontaneous mutant selection (FSMS), mutant prevention concentration (MPC), dominant mutant prevention concentration (MPC-D), inferior-mutant prevention concentration (MPC-F), and minimal selective concentration (MSC). The utility of various adaptive laboratory evolution (ALE) approaches (serial transfer, continuous culture, and evolution in spatiotemporal microenvironments) for comparing hits in terms of the level and time required for multistep resistance to emerge is discussed. We also consider how the hit-to-lead stage can benefit from high-throughput ALE setups based on robotic workstations, do-it-yourself (DIY) continuous cultivation systems, microbial evolution and growth arena (MEGA) plates, soft agar gradient evolution (SAGE) plates, microfluidic chips, or microdroplet technology. Finally, approaches for evaluating the fitness of in vitro-generated resistant mutants are presented. This review aims to draw attention to newly emerged ideas on how to improve the in vitro forecasting of the potential of compounds to select for resistance in natural settings.
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Affiliation(s)
- Joanna Krajewska
- Department of Environmental Health and Safety, National Institute of Public Health NIH—National Research Institute, 00-791 Warsaw, Poland;
| | - Stefan Tyski
- Department of Pharmaceutical Microbiology and Laboratory Diagnostic, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Agnieszka E. Laudy
- Department of Pharmaceutical Microbiology and Bioanalysis, Medical University of Warsaw, 02-097 Warsaw, Poland
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2
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Matteau D, Duval A, Baby V, Rodrigue S. Mesoplasma florum: a near-minimal model organism for systems and synthetic biology. Front Genet 2024; 15:1346707. [PMID: 38404664 PMCID: PMC10884336 DOI: 10.3389/fgene.2024.1346707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024] Open
Abstract
Mesoplasma florum is an emerging model organism for systems and synthetic biology due to its small genome (∼800 kb) and fast growth rate. While M. florum was isolated and first described almost 40 years ago, many important aspects of its biology have long remained uncharacterized due to technological limitations, the absence of dedicated molecular tools, and since this bacterial species has not been associated with any disease. However, the publication of the first M. florum genome in 2004 paved the way for a new era of research fueled by the rise of systems and synthetic biology. Some of the most important studies included the characterization and heterologous use of M. florum regulatory elements, the development of the first replicable plasmids, comparative genomics and transposon mutagenesis, whole-genome cloning in yeast, genome transplantation, in-depth characterization of the M. florum cell, as well as the development of a high-quality genome-scale metabolic model. The acquired data, knowledge, and tools will greatly facilitate future genome engineering efforts in M. florum, which could next be exploited to rationally design and create synthetic cells to advance fundamental knowledge or for specific applications.
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Affiliation(s)
- Dominick Matteau
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Anthony Duval
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Vincent Baby
- Centre de diagnostic vétérinaire de l'Université de Montréal, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Sébastien Rodrigue
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
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3
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Nguyen DK, Nguyen HQ, Dang HTT, Nguyen VQ, Nguyen L. A low-cost system for monitoring pH, dissolved oxygen and algal density in continuous culture of microalgae. HARDWAREX 2022; 12:e00353. [PMID: 36082147 PMCID: PMC9445390 DOI: 10.1016/j.ohx.2022.e00353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In a continuous and closed system of culturing microalgae, constantly monitoring and controlling pH, dissolved oxygen (DO) and microalgal density in the cultivation environment are paramount, which ultimately influence on the growth rate and quality of the microalgae products. Apart from the pH and DO parameters, the density of microalgae can be used to contemplate what light condition in the culture chamber is or when nutrients should be supplemented, which both also decide productivity of the cultivation. Moreover, the microalgal density is considered as an indicator indicating when the microalgae can be harvested. Therefore, this work proposes a low-cost monitoring equipment that can be employed to observe pH, DO and microalgal density over time in a culture environment. The measurements obtained by the proposed monitoring device can be utilized for not only real-time observations but also controlling other sub-systems in a continuous culture model including stirring, ventilating, nutrient supplying and harvesting, which leads to more efficiency in the microalgal production. More importantly, it is proposed to utilize the off-the-shelf materials to fabricate the equipment with a total cost of about 513 EUR, which makes it practical as well as widespread. The proposed monitoring apparatus was validated in a real-world closed system of cultivating a microalgae strain of Chlorella vulgaris. The obtained results indicate that the measurement accuracies are 0.3%, 3.8% and 8.6% for pH, DO and microalgae density quantities, respectively.
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Affiliation(s)
- Dung Kim Nguyen
- Faculty of Engineering, Vietnam National University of Agriculture, Hanoi 10000, Viet Nam
| | - Huy Quang Nguyen
- Faculty of Engineering, Vietnam National University of Agriculture, Hanoi 10000, Viet Nam
| | - Huyen Thuy T. Dang
- Faculty of Engineering, Vietnam National University of Agriculture, Hanoi 10000, Viet Nam
| | - Viet Quoc Nguyen
- Faculty of Engineering, Vietnam National University of Agriculture, Hanoi 10000, Viet Nam
| | - Linh Nguyen
- Institute of Innovation, Science and Sustainability, Federation University, Churchill, VIC 3842, Australia
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4
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Chee WKD, Yeoh JW, Dao VL, Poh CL. Thermogenetics: Applications come of age. Biotechnol Adv 2022; 55:107907. [PMID: 35041863 DOI: 10.1016/j.biotechadv.2022.107907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/13/2021] [Accepted: 01/09/2022] [Indexed: 12/20/2022]
Abstract
Temperature is a ubiquitous physical cue that is non-invasive, penetrative and easy to apply. In the growing field of thermogenetics, through beneficial repurposing of natural thermosensing mechanisms, synthetic biology is bringing new opportunities to design and build robust temperature-sensitive (TS) sensors which forms a thermogenetic toolbox of well characterised biological parts. Recent advancements in technological platforms available have expedited the discovery of novel or de novo thermosensors which are increasingly deployed in many practical temperature-dependent biomedical, industrial and biosafety applications. In all, the review aims to convey both the exhilarating recent technological developments underlying the advancement of thermosensors and the exciting opportunities the nascent thermogenetic field holds for biomedical and biotechnology applications.
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Affiliation(s)
- Wai Kit David Chee
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jing Wui Yeoh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Viet Linh Dao
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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5
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Lachance J, Matteau D, Brodeur J, Lloyd CJ, Mih N, King ZA, Knight TF, Feist AM, Monk JM, Palsson BO, Jacques P, Rodrigue S. Genome-scale metabolic modeling reveals key features of a minimal gene set. Mol Syst Biol 2021; 17:e10099. [PMID: 34288418 PMCID: PMC8290834 DOI: 10.15252/msb.202010099] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 12/19/2022] Open
Abstract
Mesoplasma florum, a fast-growing near-minimal organism, is a compelling model to explore rational genome designs. Using sequence and structural homology, the set of metabolic functions its genome encodes was identified, allowing the reconstruction of a metabolic network representing ˜ 30% of its protein-coding genes. Growth medium simplification enabled substrate uptake and product secretion rate quantification which, along with experimental biomass composition, were integrated as species-specific constraints to produce the functional iJL208 genome-scale model (GEM) of metabolism. Genome-wide expression and essentiality datasets as well as growth data on various carbohydrates were used to validate and refine iJL208. Discrepancies between model predictions and observations were mechanistically explained using protein structures and network analysis. iJL208 was also used to propose an in silico reduced genome. Comparing this prediction to the minimal cell JCVI-syn3.0 and its parent JCVI-syn1.0 revealed key features of a minimal gene set. iJL208 is a stepping-stone toward model-driven whole-genome engineering.
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Affiliation(s)
| | - Dominick Matteau
- Département de BiologieUniversité de SherbrookeSherbrookeQCCanada
| | - Joëlle Brodeur
- Département de BiologieUniversité de SherbrookeSherbrookeQCCanada
| | - Colton J Lloyd
- Department of BioengineeringUniversity of CaliforniaSan Diego, La JollaCAUSA
| | - Nathan Mih
- Department of BioengineeringUniversity of CaliforniaSan Diego, La JollaCAUSA
| | - Zachary A King
- Department of BioengineeringUniversity of CaliforniaSan Diego, La JollaCAUSA
| | | | - Adam M Feist
- Department of BioengineeringUniversity of CaliforniaSan Diego, La JollaCAUSA
- Department of PediatricsUniversity of CaliforniaSan Diego, La JollaCAUSA
| | - Jonathan M Monk
- Department of BioengineeringUniversity of CaliforniaSan Diego, La JollaCAUSA
| | - Bernhard O Palsson
- Department of BioengineeringUniversity of CaliforniaSan Diego, La JollaCAUSA
- Department of PediatricsUniversity of CaliforniaSan Diego, La JollaCAUSA
- Bioinformatics and Systems Biology ProgramUniversity of CaliforniaSan Diego, La JollaCAUSA
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
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6
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Leyn SA, Zlamal JE, Kurnasov OV, Li X, Elane M, Myjak L, Godzik M, de Crecy A, Garcia-Alcalde F, Ebeling M, Osterman AL. Experimental evolution in morbidostat reveals converging genomic trajectories on the path to triclosan resistance. Microb Genom 2021; 7. [PMID: 33945454 PMCID: PMC8209735 DOI: 10.1099/mgen.0.000553] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Understanding the dynamics and mechanisms of acquired drug resistance across major classes of antibiotics and bacterial pathogens is of critical importance for the optimization of current anti-infective therapies and the development of novel ones. To systematically address this challenge, we developed a workflow combining experimental evolution in a morbidostat continuous culturing device with deep genomic sequencing of population samples collected in time series. This approach was applied to the experimental evolution of six populations of Escherichia coli BW25113 towards acquiring resistance to triclosan (TCS), an antibacterial agent in various consumer products. This study revealed the rapid emergence and expansion (up to 100% in each culture within 4 days) of missense mutations in the fabI gene, encoding enoyl-acyl carrier protein reductase, the known TCS molecular target. A follow-up analysis of isolated clones showed that distinct amino acid substitutions increased the drug IC90 in a 3-16-fold range, reflecting their proximity to the TCS-binding site. In contrast to other antibiotics, efflux-upregulating mutations occurred only rarely and with low abundance. Mutations in several other genes were detected at an earlier stage of evolution. Most notably, three distinct amino acid substitutions were mapped in the C-terminal periplasmic domain of CadC protein, an acid stress-responsive transcriptional regulator. While these mutations do not confer robust TCS resistance, they appear to play a certain, yet unknown, role in adaptation to relatively low drug pressure. Overall, the observed evolutionary trajectories suggest that the FabI enzyme is the sole target of TCS (at least up to the ~50 µm level), and amino acid substitutions in the TCS-binding site represent the main mechanism of robust TCS resistance in E. coli. This model study illustrates the potential utility of the established morbidostat-based approach for uncovering resistance mechanisms and target identification for novel drug candidates with yet unknown mechanisms of action.
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Affiliation(s)
- Semen A Leyn
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jaime E Zlamal
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Oleg V Kurnasov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Xiaoqing Li
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Marinela Elane
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Lourdes Myjak
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Mikolaj Godzik
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Fernando Garcia-Alcalde
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center, Basel, Switzerland
| | - Martin Ebeling
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, Basel, Switzerland
| | - Andrei L Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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7
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Wu Y, Jameel A, Xing XH, Zhang C. Advanced strategies and tools to facilitate and streamline microbial adaptive laboratory evolution. Trends Biotechnol 2021; 40:38-59. [PMID: 33958227 DOI: 10.1016/j.tibtech.2021.04.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/17/2021] [Accepted: 04/01/2021] [Indexed: 12/18/2022]
Abstract
Adaptive laboratory evolution (ALE) has served as a historic microbial engineering method that mimics natural selection to obtain desired microbes. The past decade has witnessed improvements in all aspects of ALE workflow, in terms of growth coupling, genotypic diversification, phenotypic selection, and genotype-phenotype mapping. The developing growth-coupling strategies facilitate ALE to a wider range of appealing traits. In vivo mutagenesis methods and multiplexed automated culture platforms open new gates to streamline its execution. Meanwhile, the application of multi-omics analyses and multiplexed genetic engineering promote efficient knowledge mining. This article provides a comprehensive and updated review of these advances, highlights newest significant applications, and discusses future improvements, aiming to provide a practical guide for implementation of novel, effective, and efficient ALE experiments.
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Affiliation(s)
- Yinan Wu
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Aysha Jameel
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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8
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Matteau D, Lachance J, Grenier F, Gauthier S, Daubenspeck JM, Dybvig K, Garneau D, Knight TF, Jacques P, Rodrigue S. Integrative characterization of the near-minimal bacterium Mesoplasma florum. Mol Syst Biol 2020; 16:e9844. [PMID: 33331123 PMCID: PMC7745072 DOI: 10.15252/msb.20209844] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/11/2022] Open
Abstract
The near-minimal bacterium Mesoplasma florum is an interesting model for synthetic genomics and systems biology due to its small genome (~ 800 kb), fast growth rate, and lack of pathogenic potential. However, fundamental aspects of its biology remain largely unexplored. Here, we report a broad yet remarkably detailed characterization of M. florum by combining a wide variety of experimental approaches. We investigated several physical and physiological parameters of this bacterium, including cell size, growth kinetics, and biomass composition of the cell. We also performed the first genome-wide analysis of its transcriptome and proteome, notably revealing a conserved promoter motif, the organization of transcription units, and the transcription and protein expression levels of all protein-coding sequences. We converted gene transcription and expression levels into absolute molecular abundances using biomass quantification results, generating an unprecedented view of the M. florum cellular composition and functions. These characterization efforts provide a strong experimental foundation for the development of a genome-scale model for M. florum and will guide future genome engineering endeavors in this simple organism.
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Affiliation(s)
- Dominick Matteau
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | | | - Frédéric Grenier
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | - Samuel Gauthier
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | | | - Kevin Dybvig
- Department of GeneticsUniversity of Alabama at BirminghamBirminghamALUSA
| | - Daniel Garneau
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
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9
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Pishbin E, Kazemzadeh A, Chimerad M, Asiaei S, Navidbakhsh M, Russom A. Frequency dependent multiphase flows on centrifugal microfluidics. LAB ON A CHIP 2020; 20:514-524. [PMID: 31898702 DOI: 10.1039/c9lc00924h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The simultaneous flow of gas and liquids in large scale conduits is an established approach to enhance the performance of different working systems under critical conditions. On the microscale, the use of gas-liquid flows is challenging due to the dominance of surface tension forces. Here, we present a technique to generate common gas-liquid flows on a centrifugal microfluidic platform. It consists of a spiral microchannel and specific micro features that allow for temporal and local control of stratified and slug flow regimes. We investigate several critical parameters that induce different gas-liquid flows and cause the transition between stratified and slug flows. We have analytically derived formulations that are compared with our experimental results to deliver a general guideline for designing specific gas-liquid flows. As an application of the gas-liquid flows in enhancing microfluidic systems' performance, we show the acceleration of the cell growth of E. coli bacteria in comparison to traditional culturing methods.
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Affiliation(s)
- Esmail Pishbin
- School of Mechanical Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Amin Kazemzadeh
- Division of Nanobiotechnology, Department of Protein Sciences, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Mohammadreza Chimerad
- School of Mechanical Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Sasan Asiaei
- School of Mechanical Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Mahdi Navidbakhsh
- School of Mechanical Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Aman Russom
- Division of Nanobiotechnology, Department of Protein Sciences, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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10
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Wang X, Zheng Z, Fu F. Steering eco-evolutionary game dynamics with manifold control. Proc Math Phys Eng Sci 2020; 476:20190643. [PMID: 32082066 PMCID: PMC7016546 DOI: 10.1098/rspa.2019.0643] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/18/2019] [Indexed: 01/06/2023] Open
Abstract
Feedback loops between population dynamics of individuals and their ecological environment are ubiquitously found in nature and have shown profound effects on the resulting eco-evolutionary dynamics. By incorporating linear environmental feedback law into the replicator dynamics of two-player games, recent theoretical studies have shed light on understanding the oscillating dynamics of the social dilemma. However, the detailed effects of more general nonlinear feedback loops in multi-player games, which are more common especially in microbial systems, remain unclear. Here, we focus on ecological public goods games with environmental feedbacks driven by a nonlinear selection gradient. Unlike previous models, multiple segments of stable and unstable equilibrium manifolds can emerge from the population dynamical systems. We find that a larger relative asymmetrical feedback speed for group interactions centred on cooperators not only accelerates the convergence of stable manifolds but also increases the attraction basin of these stable manifolds. Furthermore, our work offers an innovative manifold control approach: by designing appropriate switching control laws, we are able to steer the eco-evolutionary dynamics to any desired population state. Our mathematical framework is an important generalization and complement to coevolutionary game dynamics, and also fills the theoretical gap in guiding the widespread problem of population state control in microbial experiments.
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Affiliation(s)
- Xin Wang
- LMIB, NLSDE, BDBC, PCL and School of Mathematical Sciences, Beihang University, Beijing 100191, People’s Republic of China
- Department of Mathematics, Dartmouth College, Hanover, NH 03755, USA
| | - Zhiming Zheng
- LMIB, NLSDE, BDBC, PCL and School of Mathematical Sciences, Beihang University, Beijing 100191, People’s Republic of China
| | - Feng Fu
- Department of Mathematics, Dartmouth College, Hanover, NH 03755, USA
- Department of Biomedical Data Science, Dartmouth College, Lebanon, NH 03756, USA
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11
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Tan ZL, Zheng X, Wu Y, Jian X, Xing X, Zhang C. In vivo continuous evolution of metabolic pathways for chemical production. Microb Cell Fact 2019; 18:82. [PMID: 31088458 PMCID: PMC6518619 DOI: 10.1186/s12934-019-1132-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/04/2019] [Indexed: 01/07/2023] Open
Abstract
Microorganisms have long been used as chemical plant to convert simple substrates into complex molecules. Various metabolic pathways have been optimised over the past few decades, but the progresses were limited due to our finite knowledge on metabolism. Evolution is a knowledge-free genetic randomisation approach, employed to improve the chemical production in microbial cell factories. However, evolution of large, complex pathway was a great challenge. The invention of continuous culturing systems and in vivo genetic diversification technologies have changed the way how laboratory evolution is conducted, render optimisation of large, complex pathway possible. In vivo genetic diversification, phenotypic selection, and continuous cultivation are the key elements in in vivo continuous evolution, where any human intervention in the process is prohibited. This approach is crucial in highly efficient evolution strategy of metabolic pathway evolution.
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Affiliation(s)
- Zheng Lin Tan
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama City, Kanagawa Prefecture, 226-8503 Japan
- Laboratory of Future Interdisciplinary Research and Science Technology, Tokyo Institute of Technology, Yokohama City, Kanagawa Prefecture, 226-8503 Japan
| | - Xiang Zheng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Yinan Wu
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Xingjin Jian
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Xinhui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
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12
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McGeachy AM, Meacham ZA, Ingolia NT. An Accessible Continuous-Culture Turbidostat for Pooled Analysis of Complex Libraries. ACS Synth Biol 2019; 8:844-856. [PMID: 30908907 DOI: 10.1021/acssynbio.8b00529] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present an accessible, robust continuous-culture turbidostat system that greatly facilitates the generation and phenotypic analysis of highly complex libraries in yeast and bacteria. Our system has many applications in genomics and systems biology; here, we demonstrate three of these uses. We first measure how the growth rate of budding yeast responds to limiting nitrogen at steady state and in a dynamically varying environment. We also demonstrate the direct selection of a diverse, genome-scale protein fusion library in liquid culture. Finally, we perform a comprehensive mutational analysis of the essential gene RPL28 in budding yeast, mapping sequence constraints on its wild-type function and delineating the binding site of the drug cycloheximide through resistance mutations. Our system can be constructed and operated with no specialized skills or equipment and applied to study genome-wide mutant pools and diverse libraries of sequence variants under well-defined growth conditions.
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Affiliation(s)
- Anna M. McGeachy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Zuriah A. Meacham
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Nicholas T. Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
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13
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Chan LCZ, Khalili Moghaddam G, Wang Z, Lowe CR. Miniaturized pH Holographic Sensors for the Monitoring of Lactobacillus casei Shirota Growth in a Microfluidic Chip. ACS Sens 2019; 4:456-463. [PMID: 30644723 DOI: 10.1021/acssensors.8b01470] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioreactors have been used both to develop new, and to improve bioprocess yields for, biopharmaceutical products. However, efforts to miniaturize bioreactors, in order to save costs and accelerate process development times, have been limited by the lack of on-site monitoring capabilities available at such scales. In this study, small volume (3 nL) nonconsumptive holographic sensors were integrated into a glass-PDMS microfluidic chip to monitor via a blue-shift in the resultant holographic replay wavelength, the change in pH during microbial growth of Lactobacillus casei ( L. casei) Shirota. Within the optimal growth pH range of L. casei, the accuracy of the miniaturized pH sensors was comparable to that of a conventional pH meter. Conceivably, this approach could be extrapolated to an array of miniaturized holographic sensors sensitive to different analytes, and thereby paving the way for reliable, real-time, noninvasive monitoring of microorganisms in a nanobioreactor.
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Affiliation(s)
- Leon C. Z. Chan
- Singapore Institute of Manufacturing Technology (SIMTech), A*STAR, 2 Fusionopolis Way, Innovis, Singapore 138634
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom
| | - Gita Khalili Moghaddam
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom
| | - Zhiping Wang
- Singapore Institute of Manufacturing Technology (SIMTech), A*STAR, 2 Fusionopolis Way, Innovis, Singapore 138634
| | - Christopher R. Lowe
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom
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A low-cost, open-source Turbidostat design for in-vivo control experiments in Synthetic Biology. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.ifacol.2019.12.265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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15
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Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
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Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
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16
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Skelding D, Hart SFM, Vidyasagar T, Pozhitkov AE, Shou W. Developing a low-cost milliliter-scale chemostat array for precise control of cellular growth. QUANTITATIVE BIOLOGY 2018; 6:129-141. [PMID: 31598380 DOI: 10.1007/s40484-018-0143-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Background Multiplexed milliliter-scale chemostats are useful for measuring cell physiology under various degrees of nutrient limitation and for carrying out evolution experiments. In each chemostat, fresh medium containing a growth rate-limiting metabolite is pumped into the culturing chamber at a constant rate, while culture effluent exits at an equal rate. Although such devices have been developed by various labs, key parameters - the accuracy, precision, and operational range of flow rate - are not explicitly characterized. Methods Here we re-purpose a published multiplexed culturing device to develop a multiplexed milliliter-scale chemostat. Flow rates for eight chambers can be independently controlled to a wide range, corresponding to population doubling times of 3~13 h, without the use of expensive feedback systems. Results Flow rates are precise, with the maximal coefficient of variation among eight chambers being less than 3%. Flow rates are accurate, with average flow rates being only slightly below targets, i.e., 3%-6% for 13-h and 0.6%-1.0% for 3-h doubling times. This deficit is largely due to evaporation and should be correctable. We experimentally demonstrate that our device allows accurate and precise quantification of population phenotypes. Conclusions We achieve precise control of cellular growth in a low-cost milliliter-scale chemostat array, and show that the achieved precision reduces the error when measuring biological processes.
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Affiliation(s)
- David Skelding
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Samuel F M Hart
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Alexander E Pozhitkov
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Wenying Shou
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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17
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New opportunities for optimal design of dynamic experiments in systems and synthetic biology. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.coisb.2018.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Baby V, Labroussaa F, Brodeur J, Matteau D, Gourgues G, Lartigue C, Rodrigue S. Cloning and Transplantation of the Mesoplasma florum Genome. ACS Synth Biol 2018; 7:209-217. [PMID: 28893065 DOI: 10.1021/acssynbio.7b00279] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cloning and transplantation of bacterial genomes is a powerful method for the creation of engineered microorganisms. However, much remains to be understood about the molecular mechanisms and limitations of this approach. We report the whole-genome cloning of Mesoplasma florum in Saccharomyces cerevisiae, and use this model to investigate the impact of a bacterial chromosome in yeast cells. Our results indicate that the cloned M. florum genome is subjected to weak transcriptional activity, and causes no significant impact on yeast growth. We also report that the M. florum genome can be transplanted into Mycoplasma capricolum without any negative impact from the putative restriction enzyme encoding gene mfl307. Using whole-genome sequencing, we observed that a small number of mutations appeared in all M. florum transplants. Mutations also arose, albeit at a lower frequency, when the M. capricolum genome was transplanted into M. capricolum recipient cells. These observations suggest that genome transplantation is mutagenic, and that this phenomenon is magnified by the use of genome donor and recipient cell belonging to different species. No difference in efficiency was detected after three successive rounds of genome transplantation, suggesting that the observed mutations were not selected during the procedure. Taken together, our results provide a more accurate picture of the events taking place during bacterial genome cloning and transplantation.
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Affiliation(s)
- Vincent Baby
- Université de Sherbrooke, Département de Biologie, 2500 Boulevard Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Fabien Labroussaa
- Université de Bordeaux, INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Joëlle Brodeur
- Université de Sherbrooke, Département de Biologie, 2500 Boulevard Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Dominick Matteau
- Université de Sherbrooke, Département de Biologie, 2500 Boulevard Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Géraldine Gourgues
- Université de Bordeaux, INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Carole Lartigue
- Université de Bordeaux, INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Sébastien Rodrigue
- Université de Sherbrooke, Département de Biologie, 2500 Boulevard Université, Sherbrooke, Québec J1K 2R1, Canada
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Hoffmann SA, Wohltat C, Müller KM, Arndt KM. A user-friendly, low-cost turbidostat with versatile growth rate estimation based on an extended Kalman filter. PLoS One 2017; 12:e0181923. [PMID: 28746418 PMCID: PMC5529016 DOI: 10.1371/journal.pone.0181923] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/28/2017] [Indexed: 01/22/2023] Open
Abstract
For various experimental applications, microbial cultures at defined, constant densities are highly advantageous over simple batch cultures. Due to high costs, however, devices for continuous culture at freely defined densities still experience limited use. We have developed a small-scale turbidostat for research purposes, which is manufactured from inexpensive components and 3D printed parts. A high degree of spatial system integration and a graphical user interface provide user-friendly operability. The used optical density feedback control allows for constant continuous culture at a wide range of densities and offers to vary culture volume and dilution rates without additional parametrization. Further, a recursive algorithm for on-line growth rate estimation has been implemented. The employed Kalman filtering approach based on a very general state model retains the flexibility of the used control type and can be easily adapted to other bioreactor designs. Within several minutes it can converge to robust, accurate growth rate estimates. This is particularly useful for directed evolution experiments or studies on metabolic challenges, as it allows direct monitoring of the population fitness.
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Affiliation(s)
- Stefan A. Hoffmann
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Christian Wohltat
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Katja M. Arndt
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- * E-mail:
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Development of oriC-Based Plasmids for Mesoplasma florum. Appl Environ Microbiol 2017; 83:AEM.03374-16. [PMID: 28115382 DOI: 10.1128/aem.03374-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/13/2017] [Indexed: 01/06/2023] Open
Abstract
The near-minimal bacterium Mesoplasma florum constitutes an attractive model for systems biology and for the development of a simplified cell chassis in synthetic biology. However, the lack of genetic engineering tools for this microorganism has limited our capacity to understand its basic biology and modify its genome. To address this issue, we have evaluated the susceptibility of M. florum to common antibiotics and developed the first generation of artificial plasmids able to replicate in this bacterium. Selected regions of the predicted M. florum chromosomal origin of replication (oriC) were used to create different plasmid versions that were tested for their transformation frequency and stability. Using polyethylene glycol-mediated transformation, we observed that plasmids harboring both rpmH-dnaA and dnaA-dnaN intergenic regions, interspaced or not with a copy of the dnaA gene, resulted in a frequency of ∼4.1 × 10-6 transformants per viable cell and were stably maintained throughout multiple generations. In contrast, plasmids containing only one M. florumoriC intergenic region or the heterologous oriC region of Mycoplasma capricolum, Mycoplasma mycoides, or Spiroplasma citri failed to produce any detectable transformants. We also developed alternative transformation procedures based on electroporation and conjugation from Escherichia coli, reaching frequencies up to 7.87 × 10-6 and 8.44 × 10-7 transformants per viable cell, respectively. Finally, we demonstrated the functionality of antibiotic resistance genes active against tetracycline, puromycin, and spectinomycin/streptomycin in M. florum Taken together, these valuable genetic tools will facilitate efforts toward building an M. florum-based near-minimal cellular chassis for synthetic biology.IMPORTANCEMesoplasma florum constitutes an attractive model for systems biology and for the development of a simplified cell chassis in synthetic biology. M. florum is closely related to the mycoides cluster of mycoplasmas, which has become a model for whole-genome cloning, genome transplantation, and genome minimization. However, M. florum shows higher growth rates than other Mollicutes, has no known pathogenic potential, and possesses a significantly smaller genome that positions this species among some of the simplest free-living organisms. So far, the lack of genetic engineering tools has limited our capacity to understand the basic biology of M. florum in order to modify its genome. To address this issue, we have evaluated the susceptibility of M. florum to common antibiotics and developed the first artificial plasmids and transformation methods for this bacterium. This represents a strong basis for ongoing genome engineering efforts using this near-minimal microorganism.
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Runge KW, Lustig AJ. Editorial: The Evolving Telomeres. Front Genet 2016; 7:50. [PMID: 27092174 PMCID: PMC4821857 DOI: 10.3389/fgene.2016.00050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/21/2016] [Indexed: 12/23/2022] Open
Affiliation(s)
- Kurt W Runge
- Department of Immunology, The Lerner Institute, Cleveland Clinic Foundation Cleveland, OH, USA
| | - Arthur J Lustig
- Department of Biochemistry and Molecular Biology, The Tulane Medical School and Tulane Cancer Center New Orleans, LA, USA
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