1
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Elahi Y, Baker MAB. Light Control in Microbial Systems. Int J Mol Sci 2024; 25:4001. [PMID: 38612810 PMCID: PMC11011852 DOI: 10.3390/ijms25074001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Light is a key environmental component influencing many biological processes, particularly in prokaryotes such as archaea and bacteria. Light control techniques have revolutionized precise manipulation at molecular and cellular levels in recent years. Bacteria, with adaptability and genetic tractability, are promising candidates for light control studies. This review investigates the mechanisms underlying light activation in bacteria and discusses recent advancements focusing on light control methods and techniques for controlling bacteria. We delve into the mechanisms by which bacteria sense and transduce light signals, including engineered photoreceptors and light-sensitive actuators, and various strategies employed to modulate gene expression, protein function, and bacterial motility. Furthermore, we highlight recent developments in light-integrated methods of controlling microbial responses, such as upconversion nanoparticles and optical tweezers, which can enhance the spatial and temporal control of bacteria and open new horizons for biomedical applications.
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2
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Ridgway WJM, Dalwadi MP, Pearce P, Chapman SJ. Motility-Induced Phase Separation Mediated by Bacterial Quorum Sensing. PHYSICAL REVIEW LETTERS 2023; 131:228302. [PMID: 38101339 DOI: 10.1103/physrevlett.131.228302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/09/2023] [Indexed: 12/17/2023]
Abstract
We study motility-induced phase separation (MIPS) in living active matter, in which cells interact through chemical signaling, or quorum sensing. In contrast to previous theories of MIPS, our multiscale continuum model accounts explicitly for genetic regulation of signal production and motility. Through analysis and simulations, we derive a new criterion for the onset of MIPS that depends on features of the genetic network. Furthermore, we identify and characterize a new type of oscillatory instability that occurs when gene regulation inside cells promotes motility in higher signal concentrations.
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Affiliation(s)
- Wesley J M Ridgway
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, United Kingdom
| | - Mohit P Dalwadi
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, United Kingdom
- Department of Mathematics, University College London, London WC1H 0AY, United Kingdom
- Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Philip Pearce
- Department of Mathematics, University College London, London WC1H 0AY, United Kingdom
- Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - S Jonathan Chapman
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, United Kingdom
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3
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Duan Y, Agudo-Canalejo J, Golestanian R, Mahault B. Dynamical Pattern Formation without Self-Attraction in Quorum-Sensing Active Matter: The Interplay between Nonreciprocity and Motility. PHYSICAL REVIEW LETTERS 2023; 131:148301. [PMID: 37862639 DOI: 10.1103/physrevlett.131.148301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/31/2023] [Indexed: 10/22/2023]
Abstract
We study a minimal model involving two species of particles interacting via quorum-sensing rules. Combining simulations of the microscopic model and linear stability analysis of the associated coarse-grained field theory, we identify a mechanism for dynamical pattern formation that does not rely on the standard route of intraspecies effective attractive interactions. Instead, our results reveal a highly dynamical phase of chasing bands induced only by the combined effects of self-propulsion and nonreciprocity in the interspecies couplings. Turning on self-attraction, we find that the system may phase separate into a macroscopic domain of such chaotic chasing bands coexisting with a dilute gas. We show that the chaotic dynamics of bands at the interfaces of this phase-separated phase results in anomalously slow coarsening.
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Affiliation(s)
- Yu Duan
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
| | - Jaime Agudo-Canalejo
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Benoît Mahault
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
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4
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Wang D, Cui F, Ren L, Tan X, Lv X, Li Q, Li J, Li T. Complete Genome Analysis Reveals the Quorum Sensing-Related Spoilage Potential of Pseudomonas fluorescens PF08, a Specific Spoilage Organism of Turbot ( Scophthalmus maximus). Front Microbiol 2022; 13:856802. [PMID: 35516425 PMCID: PMC9062736 DOI: 10.3389/fmicb.2022.856802] [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] [Received: 01/17/2022] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas fluorescens is a common specific spoilage organism (SSO) of aquatic products. The spoilage ability of SSO can be regulated by the quorum sensing (QS) system. However, the QS system in P. fluorescens and their relationship with the spoilage potential have not been systematically analyzed. In the present study, the complete genome of P. fluorescens PF08 isolated from spoilage turbot was sequenced. The identification of key genes that involved in the QS, enzyme synthesis, sulfur, and amino acid metabolism explained the spoilage potential of P. fluorescens PF08. Results of quantitative real-time PCR revealed the key role of the P. fluorescens PF08 QS system in regulating the transcription of spoilage-related genes and its sensitivity to environmental stress. These findings provide insight into the spoilage features of P. fluorescens PF08 from a genomic perspective. The knowledge may be valuable in the development of new strategies for the targeted inhibition of aquatic product spoilage based on QS interference.
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Affiliation(s)
- Dangfeng Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, China.,College of Food Science and Technology, Bohai University, Jinzhou, China.,National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Fangchao Cui
- College of Food Science and Technology, Bohai University, Jinzhou, China.,National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Likun Ren
- Key Laboratory of Food Science and Engineering of Heilongjiang Province, College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Xiqian Tan
- College of Food Science and Technology, Bohai University, Jinzhou, China.,National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Xinran Lv
- College of Food Science and Technology, Bohai University, Jinzhou, China.,National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Qiuying Li
- College of Food Science and Technology, Bohai University, Jinzhou, China.,National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Jianrong Li
- School of Food Science and Technology, Jiangnan University, Wuxi, China.,College of Food Science and Technology, Bohai University, Jinzhou, China.,National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Tingting Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Minzu University, Dalian, China
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5
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Zhang J, Luo Y, Poh CL. Blue Light-Directed Cell Migration, Aggregation, and Patterning. J Mol Biol 2020; 432:3137-3148. [PMID: 32247761 DOI: 10.1016/j.jmb.2020.03.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/19/2020] [Accepted: 03/26/2020] [Indexed: 12/17/2022]
Abstract
Bacterial motility is related to many cellular activities, such as cell migration, aggregation, and biofilm formations. The ability to control motility and direct the bacteria to certain location could be used to guide the bacteria in applications such as seeking for and killing pathogen, forming various population-level patterns, and delivering of drugs and vaccines. Currently, bacteria motility is mainly controlled by chemotaxis (prescribed chemical stimuli), which needs physical contact with the chemical inducer. This lacks the flexibility for pattern formation as it has limited spatial control. To overcome the limitations, we developed blue light-regulated synthetic genetic circuit to control bacterial directional motility, by taking the advantage that light stimulus can be delivered to cells in different patterns with precise spatial control. The circuit developed enables programmed Escherichia coli cells to increase directional motility and move away from the blue light, i.e., that negative phototaxis is utilized. This further allows the control of the cells to form aggregation with different patterns. Further, we showed that the circuit can be used to separate two different strains. The demonstrated ability of blue light-controllable gene circuits to regulate a CheZ expression could give researchers more means to control bacterial motility and pattern formation.
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Affiliation(s)
- Jingyun Zhang
- 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
| | - Yuhuan Luo
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, 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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6
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McKay R, Hauk P, Wu HC, Pottash AE, Shang W, Terrell J, Payne GF, Bentley WE. Controlling localization of Escherichia coli populations using a two-part synthetic motility circuit: An accelerator and brake. Biotechnol Bioeng 2017; 114:2883-2895. [PMID: 28755474 DOI: 10.1002/bit.26391] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/21/2017] [Accepted: 07/23/2017] [Indexed: 12/30/2022]
Abstract
Probiotics, whether taken as capsules or consumed in foods, have been regarded as safe for human use by regulatory agencies. Being living cells, they serve as "tunable" factories for the synthesis of a vast array of beneficial molecules. The idea of reprogramming probiotics to act as controllable factories, producing potential therapeutic molecules under user-specified conditions, represents a new and powerful concept in drug synthesis and delivery. Probiotics that serve as drug delivery vehicles pose several challenges, one being targeting (as seen with nanoparticle approaches). Here, we employ synthetic biology to control swimming directionality in a process referred to as "pseudotaxis." Escherichia coli, absent the motility regulator cheZ, swim sporadically, missing the traditional "run" in the run:tumble swimming paradigm. Upon introduction of cheZ in trans and its signal-generated upregulation, engineered bacteria can be "programmed" to swim toward the source of the chemical cue. Here, engineered cells that encounter sufficient levels of the small signal molecule pyocyanin, produce an engineered CheZ and swim with programmed directionality. By incorporating a degradation tag at the C-terminus of CheZ, the cells stop running when they exit spaces containing pyocyanin. That is, the engineered CheZ modified with a C-terminal extension derived from the putative DNA-binding transcriptional regulator YbaQ (RREERAAKKVA) is consumed by the ClpXP protease machine at a rate sufficient to "brake" the cells when pyocyanin levels are too low. Through this process, we demonstrate that over time, these engineered E. coli accumulate in pyocyanin-rich locales. We suggest that such approaches may find utility in engineering probiotics so that their beneficial functions can be focused in areas of principal benefit.
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Affiliation(s)
- Ryan McKay
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - Pricila Hauk
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei City, Taiwan
| | - Alex Eli Pottash
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Wu Shang
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | | | - Gregory F Payne
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
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7
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Transcriptional control of motility enables directional movement of Escherichia coli in a signal gradient. Sci Rep 2017; 7:8959. [PMID: 28827562 PMCID: PMC5566481 DOI: 10.1038/s41598-017-08870-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/18/2017] [Indexed: 11/08/2022] Open
Abstract
Manipulation of cellular motility using a target signal can facilitate the development of biosensors or microbe-powered biorobots. Here, we engineered signal-dependent motility in Escherichia coli via the transcriptional control of a key motility gene. Without manipulating chemotaxis, signal-dependent switching of motility, either on or off, led to population-level directional movement of cells up or down a signal gradient. We developed a mathematical model that captures the behaviour of the cells, enables identification of key parameters controlling system behaviour, and facilitates predictive-design of motility-based pattern formation. We demonstrated that motility of the receiver strains could be controlled by a sender strain generating a signal gradient. The modular quorum sensing-dependent architecture for interfacing different senders with receivers enabled a broad range of systems-level behaviours. The directional control of motility, especially combined with the potential to incorporate tuneable sensors and more complex sensing-logic, may lead to tools for novel biosensing and targeted-delivery applications.
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8
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Tien SM, Hsu CY, Chen BS. Engineering Bacteria to Search for Specific Concentrations of Molecules by a Systematic Synthetic Biology Design Method. PLoS One 2016; 11:e0152146. [PMID: 27096615 PMCID: PMC4838244 DOI: 10.1371/journal.pone.0152146] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/09/2016] [Indexed: 11/18/2022] Open
Abstract
Bacteria navigate environments full of various chemicals to seek favorable places for survival by controlling the flagella’s rotation using a complicated signal transduction pathway. By influencing the pathway, bacteria can be engineered to search for specific molecules, which has great potential for application to biomedicine and bioremediation. In this study, genetic circuits were constructed to make bacteria search for a specific molecule at particular concentrations in their environment through a synthetic biology method. In addition, by replacing the “brake component” in the synthetic circuit with some specific sensitivities, the bacteria can be engineered to locate areas containing specific concentrations of the molecule. Measured by the swarm assay qualitatively and microfluidic techniques quantitatively, the characteristics of each “brake component” were identified and represented by a mathematical model. Furthermore, we established another mathematical model to anticipate the characteristics of the “brake component”. Based on this model, an abundant component library can be established to provide adequate component selection for different searching conditions without identifying all components individually. Finally, a systematic design procedure was proposed. Following this systematic procedure, one can design a genetic circuit for bacteria to rapidly search for and locate different concentrations of particular molecules by selecting the most adequate “brake component” in the library. Moreover, following simple procedures, one can also establish an exclusive component library suitable for other cultivated environments, promoter systems, or bacterial strains.
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Affiliation(s)
- Shin-Ming Tien
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Yuan Hsu
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Bor-Sen Chen
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail:
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9
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Jung J, Park W. Acinetobacter species as model microorganisms in environmental microbiology: current state and perspectives. Appl Microbiol Biotechnol 2015; 99:2533-48. [PMID: 25693672 DOI: 10.1007/s00253-015-6439-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 01/11/2023]
Abstract
Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.
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Affiliation(s)
- Jaejoon Jung
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
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10
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Kim J, Park W. Indole inhibits bacterial quorum sensing signal transmission by interfering with quorum sensing regulator folding. MICROBIOLOGY-SGM 2013; 159:2616-2625. [PMID: 24025605 DOI: 10.1099/mic.0.070615-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quorum sensing (QS)-dependent biofilm formation and motility were controlled by AqsR in Acinetobacter oleivorans DR1. QS-controlled phenotypes appeared to be inhibited by indole and the aqsR mutant had the same phenotypes. We demonstrated that the turnover rate of AqsR became more rapid without the N-acylhomoserine lactone (AHL) signal, and that indole could increase the expression of many protease and chaperone proteins. The addition of exogenous indole decreased the expression of two AqsR-targeted genes: AOLE_03905 (putative surface adhesion protein) and AOLE_11355 (L-asparaginase). The overexpression of AqsR in Escherichia coli was impossible with the indole treatment. Surprisingly, our [(35)S]methionine pulse-labelling data demonstrated that the stability and folding of AqsR protein decreased in the presence of indole without changing aqsR mRNA expression in E. coli. Interestingly, indole resulted in a loss of TraR-dependent traG expression in an Agrobacterium tumefaciens indicator strain. However, when indole was added after incubation with exogenous AHL, indole could not inhibit the TraR-dependent expression of the traG promoter. This indicated that AHL-bound TraR could be protective against indole, but TraR without AHL could not be active in the presence of indole. Here, we provided evidence for the first time showing that the indole effect on QS-controlled bacterial phenotypes is due to inhibited QS regulator folding and not a reduced QS signal.
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Affiliation(s)
- Jisun Kim
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - Woojun Park
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
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11
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Kim J, Park W. Identification and characterization of genes regulated by AqsR, a LuxR-type regulator in Acinetobacter oleivorans DR1. Appl Microbiol Biotechnol 2013; 97:6967-78. [DOI: 10.1007/s00253-013-5006-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 05/09/2013] [Accepted: 05/17/2013] [Indexed: 12/25/2022]
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12
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Abstract
Microorganisms and specifically motile bacteria have been recently added to the list of micro-actuators typically considered for the implementation of microsystems and microrobots. Such trend has been motivated by the fact these microorganisms are self-powered actuators with overall sizes at the lower end of the micrometer range and which have proven to be extremely effective in low Reynolds number hydrodynamic regime of usually less than 10(-2). Furthermore, the various sensors or taxes in bacteria influencing their movements can also be exploited to perform tasks that were previously considered only for futuristic artificial microrobots. Bacterial implementations and related issues are not only reviewed, but this paper also proposes many techniques and approaches that can be considered as building blocks for the implementations of more sophisticated microsystems and microrobots.
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13
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Carter KK, Valdes JJ, Bentley WE. Pathway engineering via quorum sensing and sRNA riboregulators—Interconnected networks and controllers. Metab Eng 2012; 14:281-8. [DOI: 10.1016/j.ymben.2011.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 10/19/2011] [Accepted: 11/27/2011] [Indexed: 11/27/2022]
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14
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Liu C, Fu X, Liu L, Ren X, Chau CKL, Li S, Xiang L, Zeng H, Chen G, Tang LH, Lenz P, Cui X, Huang W, Hwa T, Huang JD. Sequential Establishment of Stripe Patterns in an Expanding Cell Population. Science 2011; 334:238-41. [PMID: 21998392 DOI: 10.1126/science.1209042] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Chenli Liu
- Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
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15
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Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli. J Mol Biol 2010; 406:215-27. [PMID: 21185306 DOI: 10.1016/j.jmb.2010.12.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2010] [Revised: 12/05/2010] [Accepted: 12/08/2010] [Indexed: 11/20/2022]
Abstract
Many applications require cells to switch between discrete phenotypic states. Here, we harness the FimBE inversion switch to flip a promoter, allowing expression to be toggled between two genes oriented in opposite directions. The response characteristics of the switch are characterized using two-color cytometry. This switch is used to toggle between orthogonal chemosensory pathways by controlling the expression of CheW and CheW*, which interact with the Tar (aspartate) and Tsr* (serine) chemoreceptors, respectively. CheW* and Tsr* each contain a mutation at their protein-protein interface such that they interact with each other. The complete genetic program containing an arabinose-inducible FimE controlling CheW/CheW* (and constitutively expressed tar/tsr*) is transformed into an Escherichia coli strain lacking all native chemoreceptors. This program enables bacteria to swim toward serine or aspartate in the absence or in the presence of arabinose, respectively. Thus, the program functions as a multiplexer with arabinose as the selector. This demonstrates the ability of synthetic genetic circuits to connect to a natural signaling network to switch between phenotypes.
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16
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Marguet P, Tanouchi Y, Spitz E, Smith C, You L. Oscillations by minimal bacterial suicide circuits reveal hidden facets of host-circuit physiology. PLoS One 2010; 5:e11909. [PMID: 20689598 PMCID: PMC2912849 DOI: 10.1371/journal.pone.0011909] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 07/02/2010] [Indexed: 01/03/2023] Open
Abstract
Synthetic biology seeks to enable programmed control of cellular behavior though engineered biological systems. These systems typically consist of synthetic circuits that function inside, and interact with, complex host cells possessing pre-existing metabolic and regulatory networks. Nevertheless, while designing systems, a simple well-defined interface between the synthetic gene circuit and the host is frequently assumed. We describe the generation of robust but unexpected oscillations in the densities of bacterium Escherichia coli populations by simple synthetic suicide circuits containing quorum components and a lysis gene. Contrary to design expectations, oscillations required neither the quorum sensing genes (luxR and luxI) nor known regulatory elements in the PluxI promoter. Instead, oscillations were likely due to density-dependent plasmid amplification that established a population-level negative feedback. A mathematical model based on this mechanism captures the key characteristics of oscillations, and model predictions regarding perturbations to plasmid amplification were experimentally validated. Our results underscore the importance of plasmid copy number and potential impact of “hidden interactions” on the behavior of engineered gene circuits - a major challenge for standardizing biological parts. As synthetic biology grows as a discipline, increasing value may be derived from tools that enable the assessment of parts in their final context.
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Affiliation(s)
- Philippe Marguet
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Yu Tanouchi
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Eric Spitz
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Cameron Smith
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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17
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Mishler DM, Topp S, Reynoso CMK, Gallivan JP. Engineering bacteria to recognize and follow small molecules. Curr Opin Biotechnol 2010; 21:653-6. [PMID: 20576425 DOI: 10.1016/j.copbio.2010.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 05/27/2010] [Indexed: 11/27/2022]
Abstract
The ability to recognize and react to specific environmental cues allows bacteria to localize to environments favorable to their survival and growth. Synthetic biologists have begun to exploit the chemosensory pathways that control cell motility to reprogram how bacteria move in response to novel signals. Reprograming is often accomplished by designing novel protein or RNA parts that respond to specific small molecules not normally recognized by the natural chemosensory pathways. Additionally, cell motility and localization can be coupled to bacterial quorum sensing, potentially allowing consortia of cells to perform complex tasks.
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Affiliation(s)
- Dennis M Mishler
- Department of Chemistry and Center for Fundamental and Applied Molecular Evolution, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
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18
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Kang YS, Park W. Trade-off between antibiotic resistance and biological fitness in Acinetobacter sp. strain DR1. Environ Microbiol 2010; 12:1304-18. [PMID: 20192959 DOI: 10.1111/j.1462-2920.2010.02175.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rifampicin, a bactericidal antibiotic drug, is routinely used to make an environmental recipient selective in laboratory-conjugation experiments. We noticed, inadvertently, that the rifampicin-resistant Acinetobacter sp. strain DR1, a recently discovered hexadecane-degrading environmental isolate, exhibited a substantial loss of quorum sensing signalling. The domesticated ampicillin-resistant strain, DR1, evidenced more dramatic phenotypic changes than were observed in the rifampicin-resistant cells: a complete loss of quorum sensing, a loss in swimming and swarming motilities, poor fimbrial expression, increased rigidity in membrane fatty acid composition and reduced hexadecane degradation capability. Interestingly, the motility of strain DR1 grown adjacent to a streptomycin-producing Streptomyces griceus was permanently abrogated, where this change was heritable and other phenotypic changes could not be detected. In this study, we have reported for the first time that the in situ acquisition of antibiotic resistance may reduce biological fitness, including losses in the production of quorum sensing signals, motility and substrate utilization, and each antibiotic is associated with different degrees of phenotypic and genetic alterations. Our data also suggested that the domestication of environmental isolates should be approached with caution, as there are phenotypic variations in antibiotic-resistant cells that might not be noticeable unless all possible phenotypic assays are conducted.
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Affiliation(s)
- Yoon-Suk Kang
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul, Korea
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Synthetic biology: tools to design, build, and optimize cellular processes. J Biomed Biotechnol 2010; 2010:130781. [PMID: 20150964 PMCID: PMC2817555 DOI: 10.1155/2010/130781] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 10/28/2009] [Indexed: 11/17/2022] Open
Abstract
The general central
dogma frames the emergent properties of life,
which make biology both necessary and difficult
to engineer. In a process engineering paradigm,
each biological process stream and process unit
is heavily influenced by regulatory interactions
and interactions with the surrounding
environment. Synthetic biology is developing the
tools and methods that will increase control
over these interactions, eventually resulting in
an integrative synthetic biology that will allow
ground-up cellular optimization. In this review,
we attempt to contextualize the areas of
synthetic biology into three tiers: (1) the
process units and associated streams of the
central dogma, (2) the intrinsic regulatory
mechanisms, and (3) the extrinsic physical and
chemical environment. Efforts at each of these
three tiers attempt to control cellular systems
and take advantage of emerging tools and
approaches. Ultimately, it will be possible to
integrate these approaches and realize the
vision of integrative synthetic biology when
cells are completely rewired for
biotechnological goals. This review will
highlight progress towards this goal as well as
areas requiring further research.
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Kaehr B, Shear JB. High-throughput design of microfluidics based on directed bacterial motility. LAB ON A CHIP 2009; 9:2632-2637. [PMID: 19704977 DOI: 10.1039/b908119d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Use of motile cells as sensors and actuators in microfabricated devices requires precise design of interfaces between living and non-living components, a process that has relied on slow revision of device architectures as prototypes are sequentially evaluated and re-designed. In this report, we describe a microdesign and fabrication approach capable of iteratively refining three-dimensional bacterial interfaces in periods as short as 10 minutes, and demonstrate its use to drive fluid transport by harnessing flagellar motion. In this approach, multiphoton excitation is used to promote protein photocrosslinking in a direct-write procedure mediated by static and dynamic masking, with the resultant microstructures serving to capture motile bacteria from the surrounding fluidic environment. Reproducible steering and patterning of flagellated E. coli cells drive microfluidic currents capable of guiding micro-objects on predictable trajectories with velocities reaching 150 microm s(-1) and achieving bulk flow through microchannels. We show that bacteria can be dynamically immobilized at specified positions, an approach that frees such devices from limitations imposed by the functional lifetime of cells. These results provide a foundation for the development of sophisticated microfluidic devices powered by cells.
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Affiliation(s)
- Bryan Kaehr
- Department of Chemistry & Biochemistry and the Institute for Cellular & Molecular Biology, The University of Texas, 1 University Station A5300, Austin, TX 78712, USA
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Engineering multicellular systems by cell-cell communication. Curr Opin Biotechnol 2009; 20:461-70. [PMID: 19733047 DOI: 10.1016/j.copbio.2009.08.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 08/07/2009] [Accepted: 08/12/2009] [Indexed: 11/23/2022]
Abstract
Synthetic biology encompasses the design of new biological parts and systems as well as the modulation of existing biological networks to generate novel functions. In recent years, increasing emphasis has been placed on the engineering of population-level behaviors using cell-cell communication. From the engineering perspective, cell-cell communication serves as a versatile regulatory module that enables coordination among cells in and between populations and facilitates the generation of reliable dynamics. In addition to exploring biological 'design principles' via the construction of increasingly complex dynamics, communication-based synthetic systems can be used as well-defined model systems to study ecological and social interactions such as competition, cooperation, and predation. Here we discuss the dynamic properties of cell-cell communication modules, how they can be engineered for synthetic circuit design, and applications of these systems.
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Paper and market watch. Biotechnol J 2008. [DOI: 10.1002/biot.200890085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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