1
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Gao T, Niu L, Wu X, Dai D, Zhou Y, Liu M, Wu K, Yu Y, Guan N, Ye H. Sonogenetics-controlled synthetic designer cells for cancer therapy in tumor mouse models. Cell Rep Med 2024; 5:101513. [PMID: 38608697 PMCID: PMC11148564 DOI: 10.1016/j.xcrm.2024.101513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 02/21/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024]
Abstract
Bacteria-based therapies are powerful strategies for cancer therapy, yet their clinical application is limited by a lack of tunable genetic switches to safely regulate the local expression and release of therapeutic cargoes. Rapid advances in remote-control technologies have enabled precise control of biological processes in time and space. We developed therapeutically active engineered bacteria mediated by a sono-activatable integrated gene circuit based on the thermosensitive transcriptional repressor TlpA39. Through promoter engineering and ribosome binding site screening, we achieved ultrasound (US)-induced protein expression and secretion in engineered bacteria with minimal noise and high induction efficiency. Specifically, delivered either intratumorally or intravenously, engineered bacteria colonizing tumors suppressed tumor growth through US-irradiation-induced release of the apoptotic protein azurin and an immune checkpoint inhibitor, a nanobody targeting programmed death-ligand 1, in different tumor mouse models. Beyond developing safe and high-performance designer bacteria for tumor therapy, our study illustrates a sonogenetics-controlled therapeutic platform that can be harnessed for bacteria-based precision medicine.
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Affiliation(s)
- Tian Gao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Lingxue Niu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Xin Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China; The Radiology Department of Shanxi Provincial People's Hospital, The Fifth Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Di Dai
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yang Zhou
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China; Wuhu Hospital, Health Science Center, East China Normal University, Middle Jiuhua Road 263, Wuhu City, China
| | - Mengyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Ke Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yuanhuan Yu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Ningzi Guan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China.
| | - Haifeng Ye
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China; Wuhu Hospital, Health Science Center, East China Normal University, Middle Jiuhua Road 263, Wuhu City, China.
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2
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Shui S, Scheller L, Correia BE. Protein-based bandpass filters for controlling cellular signaling with chemical inputs. Nat Chem Biol 2024; 20:586-593. [PMID: 37957273 PMCID: PMC11062894 DOI: 10.1038/s41589-023-01463-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 09/29/2023] [Indexed: 11/15/2023]
Abstract
Biological signal processing is vital for cellular function. Similar to electronic circuits, cells process signals via integrated mechanisms. In electronics, bandpass filters transmit frequencies with defined ranges, but protein-based counterparts for controlled responses are lacking in engineered biological systems. Here, we rationally design protein-based, chemically responsive bandpass filters (CBPs) showing OFF-ON-OFF patterns that respond to chemical concentrations within a specific range and reject concentrations outside that range. Employing structure-based strategies, we designed a heterodimeric construct that dimerizes in response to low concentrations of a small molecule (ON), and dissociates at high concentrations of the same molecule (OFF). The CBPs have a multidomain architecture in which we used known drug receptors, a computationally designed protein binder and small-molecule inhibitors. This modular system allows fine-tuning for optimal performance in terms of bandwidth, response, cutoff and fold changes. The CBPs were used to regulate cell surface receptor signaling pathways to control cellular activities in engineered cells.
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Affiliation(s)
- Sailan Shui
- Laboratory of Protein Design and Immunoengineering (LPDI)-STI-EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Leo Scheller
- Laboratory of Protein Design and Immunoengineering (LPDI)-STI-EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering (LPDI)-STI-EPFL, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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3
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Chen X, He C, Zhang Q, Bayakmetov S, Wang X. Modularized Design and Construction of Tunable Microbial Consortia with Flexible Topologies. ACS Synth Biol 2024; 13:183-194. [PMID: 38166159 PMCID: PMC10805104 DOI: 10.1021/acssynbio.3c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 01/04/2024]
Abstract
Complex and fluid bacterial community compositions are critical to diversity, stability, and function. However, quantitative and mechanistic descriptions of the dynamics of such compositions are still lacking. Here, we develop a modularized design framework that allows for bottom-up construction and the study of synthetic bacterial consortia with different topologies. We showcase the microbial consortia design and building process by constructing amensalism and competition consortia using only genetic circuit modules to engineer different strains to form the community. Functions of modules and hosting strains are validated and quantified to calibrate dynamic parameters, which are then directly fed into a full mechanistic model to accurately predict consortia composition dynamics for both amensalism and competition without further fitting. More importantly, such quantitative understanding successfully identifies the experimental conditions to achieve coexistence composition dynamics. These results illustrate the process of both computationally and experimentally building up bacteria consortia complexity and hence achieve robust control of such fluid systems.
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Affiliation(s)
- Xingwen Chen
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Changhan He
- Department
of Mathematics, University of California
Irvine, Irvine, California 92697, United States
| | - Qi Zhang
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Samat Bayakmetov
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiao Wang
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
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4
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Otero-Muras I, Perez-Carrasco R, Banga JR, Barnes CP. Automated design of gene circuits with optimal mushroom-bifurcation behavior. iScience 2023; 26:106836. [PMID: 37255663 PMCID: PMC10225937 DOI: 10.1016/j.isci.2023.106836] [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: 04/05/2022] [Revised: 09/20/2022] [Accepted: 05/04/2023] [Indexed: 06/01/2023] Open
Abstract
Recent advances in synthetic biology are enabling exciting technologies, including the next generation of biosensors, the rational design of cell memory, modulated synthetic cell differentiation, and generic multifunctional biocircuits. These novel applications require the design of gene circuits leading to sophisticated behaviors and functionalities. At the same time, designs need to be kept minimal to avoid compromising cell viability. Bifurcation theory addresses such challenges by associating circuit dynamical properties with molecular details of its design. Nevertheless, incorporating bifurcation analysis into automated design processes has not been accomplished yet. This work presents an optimization-based method for the automated design of synthetic gene circuits with specified bifurcation diagrams that employ minimal network topologies. Using this approach, we designed circuits exhibiting the mushroom bifurcation, distilled the most robust topologies, and explored its multifunctional behavior. We then outline potential applications in biosensors, memory devices, and synthetic cell differentiation.
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Affiliation(s)
- Irene Otero-Muras
- Computational Synthetic Biology Group. Institute for Integrative Systems Biology (UV, CSIC), Spanish National Research Council, 46980 Valencia, Spain
| | | | - Julio R. Banga
- Computational Biology Lab, MBG-CSIC, Spanish National Research Council, 36143 Pontevedra, Spain
| | - Chris P. Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
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5
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Jeong Y, Kong W, Lu T, Irudayaraj J. Soft hydrogel-shell confinement systems as bacteria-based bioactuators and biosensors. Biosens Bioelectron 2023; 219:114809. [PMID: 36274428 DOI: 10.1016/j.bios.2022.114809] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/25/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
Genetically engineered (GE) bacteria were utilized for developing functional systems upon confinement within a restricted space. Use of natural soft hydrogel such as alginate, gelatin, and agarose, have been investigated as promising approaches to design functional architectures. Nevertheless, a challenge is to develop functional microenvironments that support biofilm-like confinement in a relevant three-dimensional (3D) format for long-term studies. We demonstrate a natural soft hydrogel bioactuator based on alginate core-shell structures (0.25-2 mm core and 50-300 μm shell thickness) that enables 3D microbial colonization upon confinement with high cell density. Specially, our study evaluates the efficiency of bacteria-functional system by recapitulating various GE bacteria which can produce common reporter proteins, to demonstrate their actuator functions as well as dynamic pair-wise interactions. The structural design of the hydrogel can endure continued growth of various bacteria colonies within the confined space for over 10 days. The total amount of cellular biomass upon hydrogel-shell confinement was increased 5-fold compared to conventional techniques without hydrogel-shell. Furthermore, the enzymatic activity increased 3.8-fold and bioluminescence signal by 8-fold compared to the responses from conventional hydrogel systems. The conceptualized platform and our workflow represent a reliable strategy with core-shell structures to develop artificial hydrogel habitats as bacteria-based functional systems for bioactuation.
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Affiliation(s)
- Yoon Jeong
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wentao Kong
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joseph Irudayaraj
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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6
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Lewis DD, Gong T, Xu Y, Tan C. Frequency dependent growth of bacteria in living materials. Front Bioeng Biotechnol 2022; 10:948483. [PMID: 36159663 PMCID: PMC9493075 DOI: 10.3389/fbioe.2022.948483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
The fusion of living bacteria and man-made materials represents a new frontier in medical and biosynthetic technology. However, the principles of bacterial signal processing inside synthetic materials with three-dimensional and fluctuating environments remain elusive. Here, we study bacterial growth in a three-dimensional hydrogel. We find that bacteria expressing an antibiotic resistance module can take advantage of ambient kinetic disturbances to improve growth while encapsulated. We show that these changes in bacterial growth are specific to disturbance frequency and hydrogel density. This remarkable specificity demonstrates that periodic disturbance frequency is a new input that engineers may leverage to control bacterial growth in synthetic materials. This research provides a systematic framework for understanding and controlling bacterial information processing in three-dimensional living materials.
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Affiliation(s)
- Daniel D. Lewis
- Department of Biomedical Engineering, University of California, Davis, CA, United States
- Integrative Genetics and Genomics, University of California, Davis, CA, United States
| | - Ting Gong
- Department of Biomedical Engineering, University of California, Davis, CA, United States
| | - Yuanwei Xu
- Department of Biomedical Engineering, Peking University, Beijing, China
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California, Davis, CA, United States
- *Correspondence: Cheemeng Tan,
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7
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Oliver Huidobro M, Tica J, Wachter GKA, Isalan M. Synthetic spatial patterning in bacteria: advances based on novel diffusible signals. Microb Biotechnol 2022; 15:1685-1694. [PMID: 34843638 PMCID: PMC9151330 DOI: 10.1111/1751-7915.13979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/14/2021] [Accepted: 11/14/2021] [Indexed: 12/22/2022] Open
Abstract
Engineering multicellular patterning may help in the understanding of some fundamental laws of pattern formation and thus may contribute to the field of developmental biology. Furthermore, advanced spatial control over gene expression may revolutionize fields such as medicine, through organoid or tissue engineering. To date, foundational advances in spatial synthetic biology have often been made in prokaryotes, using artificial gene circuits. In this review, engineered patterns are classified into four levels of increasing complexity, ranging from spatial systems with no diffusible signals to systems with complex multi-diffusor interactions. This classification highlights how the field was held back by a lack of diffusible components. Consequently, we provide a summary of both previously characterized and some new potential candidate small-molecule signals that can regulate gene expression in Escherichia coli. These diffusive signals will help synthetic biologists to successfully engineer increasingly intricate, robust and tuneable spatial structures.
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Affiliation(s)
| | - Jure Tica
- Department of Life SciencesImperial College LondonLondonSW7 2AZUK
| | | | - Mark Isalan
- Department of Life SciencesImperial College LondonLondonSW7 2AZUK
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8
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Peter SB, Qiao Z, Godspower HN, Ajeje SB, Xu M, Zhang X, Yang T, Rao Z. Biotechnological Innovations and Therapeutic Application of Pediococcus and Lactic Acid Bacteria: The Next-Generation Microorganism. Front Bioeng Biotechnol 2022; 9:802031. [PMID: 35237589 PMCID: PMC8883390 DOI: 10.3389/fbioe.2021.802031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/08/2021] [Indexed: 01/27/2023] Open
Abstract
Lactic acid bacteria represent a worthwhile organism within the microbial consortium for the food sector, health, and biotechnological applications. They tend to offer high stability to environmental conditions, with an indicated increase in product yield, alongside their moderate antimicrobial activity. Lack of endotoxins and inclusion bodies, extracellular secretion, and surface display with other unique properties, are all winning attributes of these Gram-positive lactic acid bacteria, of which, Pediococcus is progressively becoming an attractive and promising host, as the next-generation probiotic comparable with other well-known model systems. Here, we presented the biotechnological developments in Pediococcal bacteriocin expression system, contemporary variegated models of Pediococcus and lactic acid bacteria strains as microbial cell factory, most recent applications as possible live delivery vector for use as therapeutics, as well as upsurging challenges and future perspective. With the radical introduction of artificial intelligence and neural network in Synthetic Biology, the microbial usage of lactic acid bacteria as an alternative eco-friendly strain, with safe use properties compared with the already known conventional strains is expected to see an increase in various food and biotechnological applications in years to come as it offers better hope of safety, accuracy, and higher efficiency.
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Affiliation(s)
- Sunday Bulus Peter
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhina Qiao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hero Nmeri Godspower
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Samaila Boyi Ajeje
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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9
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Winkle JJ, Karamched BR, Bennett MR, Ott W, Josić K. Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia. PLoS Comput Biol 2021; 17:e1009381. [PMID: 34550968 PMCID: PMC8489724 DOI: 10.1371/journal.pcbi.1009381] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 10/04/2021] [Accepted: 08/25/2021] [Indexed: 12/04/2022] Open
Abstract
The increased complexity of synthetic microbial biocircuits highlights the need for distributed cell functionality due to concomitant increases in metabolic and regulatory burdens imposed on single-strain topologies. Distributed systems, however, introduce additional challenges since consortium composition and spatiotemporal dynamics of constituent strains must be robustly controlled to achieve desired circuit behaviors. Here, we address these challenges with a modeling-based investigation of emergent spatiotemporal population dynamics using cell-length control in monolayer, two-strain bacterial consortia. We demonstrate that with dynamic control of a strain's division length, nematic cell alignment in close-packed monolayers can be destabilized. We find that this destabilization confers an emergent, competitive advantage to smaller-length strains-but by mechanisms that differ depending on the spatial patterns of the population. We used complementary modeling approaches to elucidate underlying mechanisms: an agent-based model to simulate detailed mechanical and signaling interactions between the competing strains, and a reductive, stochastic lattice model to represent cell-cell interactions with a single rotational parameter. Our modeling suggests that spatial strain-fraction oscillations can be generated when cell-length control is coupled to quorum-sensing signaling in negative feedback topologies. Our research employs novel methods of population control and points the way to programming strain fraction dynamics in consortial synthetic biology.
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Affiliation(s)
- James J Winkle
- Department of Mathematics, University of Houston, Houston, Texas, United States of America
| | - Bhargav R Karamched
- Department of Mathematics, Florida State University, Tallahassee, Florida, United States of America
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America
| | - Matthew R Bennett
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - William Ott
- Department of Mathematics, University of Houston, Houston, Texas, United States of America
| | - Krešimir Josić
- Department of Mathematics, University of Houston, Houston, Texas, United States of America
- Department of Biosciences, Rice University, Houston, Texas, United States of America
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
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10
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Abstract
Microorganisms live in dense and diverse communities, with interactions between cells guiding community development and phenotype. The ability to perturb specific intercellular interactions in space and time provides a powerful route to determining the critical interactions and design rules for microbial communities. Approaches using optogenetic tools to modulate these interactions offer promise, as light can be exquisitely controlled in space and time. We report new plasmids for rapid integration of an optogenetic system into Saccharomyces cerevisiae to engineer light control of expression of a gene of interest. In a proof-of-principle study, we demonstrate the ability to control a model cooperative interaction, namely, the expression of the enzyme invertase (SUC2) which allows S. cerevisiae to hydrolyze sucrose and utilize it as a carbon source. We demonstrate that the strength of this cooperative interaction can be tuned in space and time by modulating light intensity and through spatial control of illumination. Spatial control of light allows cooperators and cheaters to be spatially segregated, and we show that the interplay between cooperative and inhibitory interactions in space can lead to pattern formation. Our strategy can be applied to achieve spatiotemporal control of expression of a gene of interest in S. cerevisiae to perturb both intercellular and interspecies interactions. IMPORTANCE Recent advances in microbial ecology have highlighted the importance of intercellular interactions in controlling the development, composition, and resilience of microbial communities. In order to better understand the role of these interactions in governing community development, it is critical to be able to alter them in a controlled manner. Optogenetically controlled interactions offer advantages over static perturbations or chemically controlled interactions, as light can be manipulated in space and time and does not require the addition of nutrients or antibiotics. Here, we report a system for rapidly achieving light control of a gene of interest in the important model organism Saccharomyces cerevisiae and demonstrate that by controlling expression of the enzyme invertase, we can control cooperative interactions. This approach will be useful for understanding intercellular and interspecies interactions in natural and synthetic microbial consortia containing S. cerevisiae and serves as a proof of principle for implementing this approach in other consortia.
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11
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Engineering AraC to make it responsive to light instead of arabinose. Nat Chem Biol 2021; 17:817-827. [PMID: 33903769 DOI: 10.1038/s41589-021-00787-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 03/19/2021] [Indexed: 02/02/2023]
Abstract
The L-arabinose-responsive AraC and its cognate PBAD promoter underlie one of the most often used chemically inducible prokaryotic gene expression systems in microbiology and synthetic biology. Here, we change the sensing capability of AraC from L-arabinose to blue light, making its dimerization and the resulting PBAD activation light-inducible. We engineer an entire family of blue light-inducible AraC dimers in Escherichia coli (BLADE) to control gene expression in space and time. We show that BLADE can be used with pre-existing L-arabinose-responsive plasmids and strains, enabling optogenetic experiments without the need to clone. Furthermore, we apply BLADE to control, with light, the catabolism of L-arabinose, thus externally steering bacterial growth with a simple transformation step. Our work establishes BLADE as a highly practical and effective optogenetic tool with plug-and-play functionality-features that we hope will accelerate the broader adoption of optogenetics and the realization of its vast potential in microbiology, synthetic biology and biotechnology.
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12
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Wang X, Harrison A. A general principle for spontaneous genetic symmetry breaking and pattern formation within cell populations. J Theor Biol 2021; 526:110809. [PMID: 34119496 DOI: 10.1016/j.jtbi.2021.110809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/23/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022]
Abstract
Elements within biological systems interact and frequently self-organize from initially disordered states into highly structured patterns. The local self-activation and lateral inhibition mechanism, derived from the coupling between two reacting and diffusing chemicals, has been believed to be one of the main causes for biological pattern formation. Graded positional information can be produced by the limited diffusion of one single signaling molecule through cell populations with no pre-patterns being required. We demonstrate, using multiscale computations, that spontaneous symmetry breaking can be driven within expanding and non-expanding cell populations, without local self-enhancement of activators and long-range inhibition. Instead, cells can self-organize into structured gene patterns via a combination of timing gene expression in cells and the graded positional information which has been coupled to the gene expression. We show that the genetic symmetry breaking in expanding E. coli populations occurs at a critical colony size, which is independent of the cell doubling time but scales with the diffusion speed of the signaling molecule. We also show the quasi-3D structure of gene patterns, and observe that the wave length of periodic genetic stripes is in proportion to the genetic oscillation cycle time and in inverse proportion to cell doubling time. Our results provide insights into relevant biological development processes.
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Affiliation(s)
- Xiaoliang Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China; School of Physical Sciences, University of Science and Technology of China, Hefei 230026, China.
| | - Andrew Harrison
- Department of Mathematical Sciences, University of Essex, Colchester CO4 3SQ, UK.
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13
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Wang X, Bai D. Self‐Organization Principles of Cell Cycles and Gene Expressions in the Development of Cell Populations. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202100005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaoliang Wang
- College of Life Sciences Zhejiang University Hangzhou 310058 China
- School of Physical Sciences University of Science and Technology of China Hefei 230026 China
| | - Dongyun Bai
- School of Physics and Astronomy Shanghai Jiao Tong University Shanghai 200240 China
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14
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Grant PK, Szep G, Patange O, Halatek J, Coppard V, Csikász-Nagy A, Haseloff J, Locke JCW, Dalchau N, Phillips A. Interpretation of morphogen gradients by a synthetic bistable circuit. Nat Commun 2020; 11:5545. [PMID: 33139718 PMCID: PMC7608687 DOI: 10.1038/s41467-020-19098-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/23/2020] [Indexed: 12/02/2022] Open
Abstract
During development, cells gain positional information through the interpretation of dynamic morphogen gradients. A proposed mechanism for interpreting opposing morphogen gradients is mutual inhibition of downstream transcription factors, but isolating the role of this specific motif within a natural network remains a challenge. Here, we engineer a synthetic morphogen-induced mutual inhibition circuit in E. coli populations and show that mutual inhibition alone is sufficient to produce stable domains of gene expression in response to dynamic morphogen gradients, provided the spatial average of the morphogens falls within the region of bistability at the single cell level. When we add sender devices, the resulting patterning circuit produces theoretically predicted self-organised gene expression domains in response to a single gradient. We develop computational models of our synthetic circuits parameterised to timecourse fluorescence data, providing both a theoretical and experimental framework for engineering morphogen-induced spatial patterning in cell populations. Morphogen gradients can be dynamic and transient yet give rise to stable cellular patterns. Here the authors show that a synthetic morphogen-induced mutual inhibition circuit produces stable boundaries when the spatial average of morphogens falls within the region of bistability.
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Affiliation(s)
- Paul K Grant
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK.
| | - Gregory Szep
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK.,Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK
| | - Om Patange
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jacob Halatek
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK
| | | | - Attila Csikász-Nagy
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK.,Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, 1083, Hungary
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - James C W Locke
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK.,Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK.,Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Neil Dalchau
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK
| | - Andrew Phillips
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK.
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15
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Karkaria BD, Treloar NJ, Barnes CP, Fedorec AJH. From Microbial Communities to Distributed Computing Systems. Front Bioeng Biotechnol 2020; 8:834. [PMID: 32793576 PMCID: PMC7387671 DOI: 10.3389/fbioe.2020.00834] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
A distributed biological system can be defined as a system whose components are located in different subpopulations, which communicate and coordinate their actions through interpopulation messages and interactions. We see that distributed systems are pervasive in nature, performing computation across all scales, from microbial communities to a flock of birds. We often observe that information processing within communities exhibits a complexity far greater than any single organism. Synthetic biology is an area of research which aims to design and build synthetic biological machines from biological parts to perform a defined function, in a manner similar to the engineering disciplines. However, the field has reached a bottleneck in the complexity of the genetic networks that we can implement using monocultures, facing constraints from metabolic burden and genetic interference. This makes building distributed biological systems an attractive prospect for synthetic biology that would alleviate these constraints and allow us to expand the applications of our systems into areas including complex biosensing and diagnostic tools, bioprocess control and the monitoring of industrial processes. In this review we will discuss the fundamental limitations we face when engineering functionality with a monoculture, and the key areas where distributed systems can provide an advantage. We cite evidence from natural systems that support arguments in favor of distributed systems to overcome the limitations of monocultures. Following this we conduct a comprehensive overview of the synthetic communities that have been built to date, and the components that have been used. The potential computational capabilities of communities are discussed, along with some of the applications that these will be useful for. We discuss some of the challenges with building co-cultures, including the problem of competitive exclusion and maintenance of desired community composition. Finally, we assess computational frameworks currently available to aide in the design of microbial communities and identify areas where we lack the necessary tools.
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Affiliation(s)
- Behzad D. Karkaria
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Neythen J. Treloar
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Chris P. Barnes
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Alex J. H. Fedorec
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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16
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Integrative Circuit-Host Modeling of a Genetic Switch in Varying Environments. Sci Rep 2020; 10:8383. [PMID: 32433471 PMCID: PMC7239927 DOI: 10.1038/s41598-020-64921-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/23/2020] [Indexed: 01/17/2023] Open
Abstract
Synthetic biology is advancing into a new phase where real-world applications are emphasized. There is hence an urgent need for mathematical modeling that can quantitatively describe the behaviors of genetic devices in natural, fluctuating environments. We utilize an integrative circuit-host modeling framework to examine the dynamics of a genetic switch and its host cell in varying environments. For both steady-state and transient cases, we find increasing nutrient reduces the bistability region of the phase space and eventually drives the switch from bistability to monostability. In response, cellular growth and proteome partitioning experience the same transition. Antibiotic perturbations cause the similar circuit and host responses as nutrient variations. However, one difference is the trend of growth rate, which augments with nutrient but declines with antibiotic levels. The framework provides a mechanistic scheme to account for both the dynamic and static characteristics of the circuit-host system upon environmental perturbations, underscoring the intimacy of gene circuits and their hosts and elucidating the complexity of circuit behaviors arising from environmental variations.
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17
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Fang K, Park OJ, Hong SH. Controlling biofilms using synthetic biology approaches. Biotechnol Adv 2020; 40:107518. [PMID: 31953206 PMCID: PMC7125041 DOI: 10.1016/j.biotechadv.2020.107518] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/09/2020] [Accepted: 01/11/2020] [Indexed: 12/22/2022]
Abstract
Bacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene expression, and secretion of extracellular polymeric substances. Given the robust nature of biofilms due to the non-growing nature of biofilm bacteria and the physical barrier provided by the extracellular matrix, eradicating biofilms is a very difficult task to accomplish with conventional antibiotic or disinfectant treatments. Synthetic biology holds substantial promise for controlling biofilms by improving and expanding existing biological tools, introducing novel functions to the system, and re-conceptualizing gene regulation. This review summarizes synthetic biology approaches used to eradicate biofilms via protein engineering of biofilm-related enzymes, utilization of synthetic genetic circuits, and the development of functional living agents. Synthetic biology also enables beneficial applications of biofilms through the production of biomaterials and patterning biofilms with specific temporal and spatial structures. Advances in synthetic biology will add novel biofilm functionalities for future therapeutic, biomanufacturing, and environmental applications.
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Affiliation(s)
- Kuili Fang
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Oh-Jin Park
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA; Department of Biological and Chemical Engineering, Yanbian University of Science and Technology, Yanji, Jilin, People's Republic of China
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA.
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18
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Bittihn P, Didovyk A, Tsimring LS, Hasty J. Genetically engineered control of phenotypic structure in microbial colonies. Nat Microbiol 2020; 5:697-705. [PMID: 32284568 DOI: 10.1038/s41564-020-0686-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 02/07/2020] [Indexed: 12/11/2022]
Abstract
Rapid advances in cellular engineering1,2 have positioned synthetic biology to address therapeutic3,4 and industrial5 problems, but a substantial obstacle is the myriad of unanticipated cellular responses in heterogeneous real-world environments such as the gut6,7, solid tumours8,9, bioreactors10 or soil11. Complex interactions between the environment and cells often arise through non-uniform nutrient availability, which generates bidirectional coupling as cells both adjust to and modify their local environment through phenotypic differentiation12,13. Although synthetic spatial gene expression patterns14-17 have been explored under homogeneous conditions, the mutual interaction of gene circuits, growth phenotype and the environment remains a challenge. Here, we design gene circuits that sense and control phenotypic structure in microcolonies containing both growing and dormant bacteria. We implement structure modulation by coupling different downstream modules to a tunable sensor that leverages Escherichia coli's stress response and is activated on growth arrest. One is an actuator module that slows growth and thereby alters nutrient gradients. Environmental feedback in this circuit generates robust cycling between growth and dormancy in the interior of the colony, as predicted by a spatiotemporal computational model. We also use the sensor to drive an inducible gating module for selective gene expression in non-dividing cells, which allows us to radically alter population structure by eliminating the dormant phenotype with a 'stress-gated lysis circuit'. Our results establish a strategy to leverage and control microbial colony structure for synthetic biology applications in complex environments.
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Affiliation(s)
- Philip Bittihn
- BioCircuits Institute, University of California, San Diego, La Jolla, CA, USA.,The San Diego Center for Systems Biology, La Jolla, CA, USA.,Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Andriy Didovyk
- BioCircuits Institute, University of California, San Diego, La Jolla, CA, USA.,Vertex Pharmaceuticals, San Diego, CA, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California, San Diego, La Jolla, CA, USA. .,The San Diego Center for Systems Biology, La Jolla, CA, USA.
| | - Jeff Hasty
- BioCircuits Institute, University of California, San Diego, La Jolla, CA, USA. .,The San Diego Center for Systems Biology, La Jolla, CA, USA. .,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. .,Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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19
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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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20
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Alnahhas RN, Winkle JJ, Hirning AJ, Karamched B, Ott W, Josić K, Bennett MR. Spatiotemporal Dynamics of Synthetic Microbial Consortia in Microfluidic Devices. ACS Synth Biol 2019; 8:2051-2058. [PMID: 31361464 PMCID: PMC6754295 DOI: 10.1021/acssynbio.9b00146] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Synthetic microbial consortia consist of two or more engineered strains that grow together and share the same resources. When intercellular signaling pathways are included in the engineered strains, close proximity of the microbes can generate complex dynamic behaviors that are difficult to obtain using a single strain. However, when a consortium is not cultured in a well-mixed environment the constituent strains passively compete for space as they grow and divide, complicating cell-cell signaling. Here, we explore the temporal dynamics of the spatial distribution of consortia cocultured in microfluidic devices. To do this, we grew two different strains of Escherichia coli in microfluidic devices with cell-trapping regions (traps) of several different designs. We found that the size of the traps is a critical determinant of spatiotemporal dynamics. In small traps, cells can easily signal one another, but the relative proportion of each strain within the trap can fluctuate wildly. In large traps, the relative ratio of strains is stabilized, but intercellular signaling can be hindered by distances between cells. This presents a trade-off between the trap size and the effectiveness of intercellular signaling, which can be mitigated by increasing the initial seeding of cells in larger traps. We also built a mathematical model, which suggests that increasing the number of seed cells can also increase the strain ratio variability due to an increased number of strain interfaces in the trap. These results help elucidate the complex behaviors of synthetic microbial consortia in microfluidic traps and provide a means of analysis to help remedy the spatial heterogeneity inherent to different trap types.
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Affiliation(s)
- Razan N Alnahhas
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - James J Winkle
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - Andrew J Hirning
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - Bhargav Karamched
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
| | - William Ott
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
| | - Krešimir Josić
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
- Department of Biology and Biochemistry , University of Houston , Houston , Texas 77004 , United States
| | - Matthew R Bennett
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
- Department of Bioengineering , Rice University , Houston , Texas 77005 , United States
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21
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Majerle A, Schmieden DT, Jerala R, Meyer AS. Synthetic Biology for Multiscale Designed Biomimetic Assemblies: From Designed Self-Assembling Biopolymers to Bacterial Bioprinting. Biochemistry 2019; 58:2095-2104. [PMID: 30957491 DOI: 10.1021/acs.biochem.8b00922] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nature is based on complex self-assembling systems that span from the nanoscale to the macroscale. We have already begun to design biomimetic systems with properties that have not evolved in nature, based on designed molecular interactions and regulation of biological systems. Synthetic biology is based on the principle of modularity, repurposing diverse building modules to design new types of molecular and cellular assemblies. While we are currently able to use techniques from synthetic biology to design self-assembling molecules and re-engineer functional cells, we still need to use guided assembly to construct biological assemblies at the macroscale. We review the recent strategies for designing biological systems ranging from molecular assemblies based on self-assembly of (poly)peptides to the guided assembly of patterned bacteria, spanning 7 orders of magnitude.
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Affiliation(s)
- Andreja Majerle
- Department of Synthetic Biology and Immunology , National Institute of Chemistry , Hajdrihova 19 , 1000 Ljubljana , Slovenia
| | - Dominik T Schmieden
- Department of Bionanoscience, Kavli Institute of Nanoscience , Delft University of Technology , 2629 HZ Delft , The Netherlands
| | - Roman Jerala
- Department of Synthetic Biology and Immunology , National Institute of Chemistry , Hajdrihova 19 , 1000 Ljubljana , Slovenia
| | - Anne S Meyer
- Department of Biology , University of Rochester , Rochester , New York 14627 , United States
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22
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Circuit-Host Coupling Induces Multifaceted Behavioral Modulations of a Gene Switch. Biophys J 2019; 114:737-746. [PMID: 29414718 DOI: 10.1016/j.bpj.2017.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/12/2017] [Accepted: 12/01/2017] [Indexed: 12/30/2022] Open
Abstract
Quantitative modeling of gene circuits is fundamentally important to synthetic biology, as it offers the potential to transform circuit engineering from trial-and-error construction to rational design and, hence, facilitates the advance of the field. Currently, typical models regard gene circuits as isolated entities and focus only on the biochemical processes within the circuits. However, such a standard paradigm is getting challenged by increasing experimental evidence suggesting that circuits and their host are intimately connected, and their interactions can potentially impact circuit behaviors. Here we systematically examined the roles of circuit-host coupling in shaping circuit dynamics by using a self-activating gene switch as a model circuit. Through a combination of deterministic modeling, stochastic simulation, and Fokker-Planck equation formalism, we found that circuit-host coupling alters switch behaviors across multiple scales. At the single-cell level, it slows the switch dynamics in the high protein production regime and enlarges the difference between stable steady-state values. At the population level, it favors cells with low protein production through differential growth amplification. Together, the two-level coupling effects induce both quantitative and qualitative modulations of the switch, with the primary component of the effects determined by the circuit's architectural parameters. This study illustrates the complexity and importance of circuit-host coupling in modulating circuit behaviors, demonstrating the need for a new paradigm-integrated modeling of the circuit-host system-for quantitative understanding of engineered gene networks.
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23
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Denton JA, Gokhale CS. Synthetic Mutualism and the Intervention Dilemma. Life (Basel) 2019; 9:E15. [PMID: 30696090 PMCID: PMC6463046 DOI: 10.3390/life9010015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/09/2019] [Accepted: 01/23/2019] [Indexed: 01/09/2023] Open
Abstract
Ecosystems are complex networks of interacting individuals co-evolving with their environment. As such, changes to an interaction can influence the whole ecosystem. However, to predict the outcome of these changes, considerable understanding of processes driving the system is required. Synthetic biology provides powerful tools to aid this understanding, but these developments also allow us to change specific interactions. Of particular interest is the ecological importance of mutualism, a subset of cooperative interactions. Mutualism occurs when individuals of different species provide a reciprocal fitness benefit. We review available experimental techniques of synthetic biology focused on engineered synthetic mutualistic systems. Components of these systems have defined interactions that can be altered to model naturally occurring relationships. Integrations between experimental systems and theoretical models, each informing the use or development of the other, allow predictions to be made about the nature of complex relationships. The predictions range from stability of microbial communities in extreme environments to the collapse of ecosystems due to dangerous levels of human intervention. With such caveats, we evaluate the promise of synthetic biology from the perspective of ethics and laws regarding biological alterations, whether on Earth or beyond. Just because we are able to change something, should we?
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Affiliation(s)
- Jai A Denton
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Onna-son 904-0412, Japan.
| | - Chaitanya S Gokhale
- Research Group for Theoretical models of Eco-Evolutionary Dynamics, Max Planck Institute for Evolutionary Biology, 24304 Plön, Germany.
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24
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Affiliation(s)
- Nan Luo
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Shangying Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, United States
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27708, United States
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25
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Engineering of lactic acid bacteria for delivery of therapeutic proteins and peptides. Appl Microbiol Biotechnol 2019; 103:2053-2066. [DOI: 10.1007/s00253-019-09628-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/11/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023]
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26
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Santos‐Moreno J, Schaerli Y. Using Synthetic Biology to Engineer Spatial Patterns. ACTA ACUST UNITED AC 2018; 3:e1800280. [DOI: 10.1002/adbi.201800280] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/14/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Javier Santos‐Moreno
- Department of Fundamental MicrobiologyUniversity of LausanneBiophore Building 1015 Lausanne Switzerland
| | - Yolanda Schaerli
- Department of Fundamental MicrobiologyUniversity of LausanneBiophore Building 1015 Lausanne Switzerland
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27
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Maddaloni M, Kochetkova I, Hoffman C, Pascual DW. Delivery of IL-35 by Lactococcus lactis Ameliorates Collagen-Induced Arthritis in Mice. Front Immunol 2018; 9:2691. [PMID: 30515168 PMCID: PMC6255909 DOI: 10.3389/fimmu.2018.02691] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/31/2018] [Indexed: 12/21/2022] Open
Abstract
IL-35, a relatively newly discovered cytokine belonging to the larger IL-12 family, shows unique anti-inflammatory properties, believed to be associated with dedicated receptors and signaling pathways. IL-35 plays a pivotal role in the development and the function of both regulatory B (Bregs) and T cells (Tregs). In order to further its therapeutic potential, a dairy Lactococcus lactis strain was engineered to express murine IL-35 (LL-IL35), and this recombinant strain was applied to suppress collagen-induced arthritis (CIA). Oral administration of LL-IL35 effectively reduced the incidence and disease severity of CIA. When administered therapeutically, LL-IL35 abruptly halted CIA progression with no increase in disease severity by reducing neutrophil influx into the joints. LL-IL35 treatment reduced IFN-γ and IL-17 3.7- and 8.5-fold, respectively, and increased IL-10 production compared to diseased mice. Foxp3+ and Foxp3- CD39+ CD4+ T cells were previously shown to be the Tregs responsible for conferring protection against CIA. Inquiry into their induction revealed that both CCR6+ and CCR6- Foxp3+or- CD39+ CD4+ T cells act as the source of the IL-10 induced by LL-IL35. Thus, this study demonstrates the feasibility and benefits of engineered probiotics for treating autoimmune diseases.
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Affiliation(s)
- Massimo Maddaloni
- Department of Infectious Diseases and Immunology, University of Florida, Gainesville, FL, United States
| | - Irina Kochetkova
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Carol Hoffman
- Department of Infectious Diseases and Immunology, University of Florida, Gainesville, FL, United States
| | - David W. Pascual
- Department of Infectious Diseases and Immunology, University of Florida, Gainesville, FL, United States
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28
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Ozdemir T, Fedorec AJ, Danino T, Barnes CP. Synthetic Biology and Engineered Live Biotherapeutics: Toward Increasing System Complexity. Cell Syst 2018; 7:5-16. [DOI: 10.1016/j.cels.2018.06.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/31/2018] [Accepted: 06/15/2018] [Indexed: 12/31/2022]
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29
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Bittihn P, Din MO, Tsimring LS, Hasty J. Rational engineering of synthetic microbial systems: from single cells to consortia. Curr Opin Microbiol 2018; 45:92-99. [PMID: 29574330 DOI: 10.1016/j.mib.2018.02.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/06/2018] [Accepted: 02/19/2018] [Indexed: 12/11/2022]
Abstract
One promise of synthetic biology is to provide solutions for biomedical and industrial problems by rational design of added functionality in living systems. Microbes are at the forefront of this biological engineering endeavor due to their general ease of handling and their relevance in many potential applications from fermentation to therapeutics. In recent years, the field has witnessed an explosion of novel regulatory tools, from synthetic orthogonal transcription factors to posttranslational mechanisms for increased control over the behavior of synthetic circuits. Tool development has been paralleled by the discovery of principles that enable increased modularity and the management of host-circuit interactions. Engineered cell-to-cell communication bridges the scales from intracellular to population-level coordination. These developments facilitate the translation of more than a decade of circuit design into applications.
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Affiliation(s)
- Philip Bittihn
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - M Omar Din
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Molecular Biology Section, Division of Biological Science, University of California, San Diego, La Jolla, CA 92093, USA.
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30
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Synthetic biology in probiotic lactic acid bacteria: At the frontier of living therapeutics. Curr Opin Biotechnol 2018; 53:224-231. [PMID: 29550614 DOI: 10.1016/j.copbio.2018.01.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/22/2017] [Accepted: 01/24/2018] [Indexed: 12/19/2022]
Abstract
The trillions of microbes hosted by humans can dictate health or illness depending on a multitude of genetic, environmental, and lifestyle factors that help define the human ecosystem. As the human microbiota is characterized, so can the interconnectivity of microbe-host-disease be realized and manipulated. Designing microbes as therapeutic agents can not only enable targeted drug delivery but also restore homeostasis within a perturbed microbial community. Used for centuries in fermentation and preservation of food, lactic acid bacteria (LAB) have a long history of safe, and occasionally health promoting, interactions with the human gut, making them ideal candidates for engineered functionality. This review outlines available genetic tools, recent developments in biomedical applications, as well as potential future applications of synthetic biology to program LAB-based therapeutic systems.
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31
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Contribution of YthA, a PspC Family Transcriptional Regulator of Lactococcus lactis F44 Acid Tolerance and Nisin Yield: a Transcriptomic Approach. Appl Environ Microbiol 2018. [PMID: 29305506 DOI: 10.1128/aem.02483-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
To overcome the adverse impacts of environmental stresses during growth, different adaptive regulation mechanisms can be activated in Lactococcus lactis In this study, the transcription levels of eight transcriptional regulators of L. lactis subsp. lactis F44 under acid stress were analyzed using quantitative reverse transcription-PCR. Eight gene-overexpressing strains were then constructed to examine their influences on acid-resistant capability. Overexpressing ythA, a PspC family transcriptional regulator, increased the survival rate by 3.2-fold compared to the control at the lethal pH 3.0 acid shock. Moreover, the nisin yield was increased by 45.50%. The ythA-overexpressing strain FythA appeared to have higher intracellular pH stability and nisin-resistant ability. Subsequently, transcriptome analysis revealed that the vast majority of genes associated with amino acid biosynthesis, including arginine, serine, phenylalanine, and tyrosine, were predominantly upregulated in FythA. Arginine biosynthesis (argG and argH), arginine deiminase pathway, and polar amino acid transport (ysfE and ysfF) were proposed to be the main regulation mechanisms of YthA. Furthermore, the transcription of genes associated with pyrimidine and exopolysaccharide biosynthesis were upregulated. The transcriptional levels of nisIPRKFEG genes were substantially higher in FythA, which directly contributed to the yield and resistance of nisin. Three potential DNA-binding sequences were predicted by computer analysis using the upstream regions of genes with prominent changes. This study showed that YthA could increase acid resistance and nisin yield and revealed a putative regulation mechanism of YthA.IMPORTANCE Nisin, produced by Lactococcus lactis subsp. lactis, is widely used as a safe food preservative. Acid stress becomes the primary restrictive factor of cell growth and nisin yield. In this research, we found that the transcriptional regulator YthA was conducive to enhancing the acid resistance of L. lactis F44. Overexpressing ythA could significantly improve the survival rate and nisin yield. The stability of intracellular pH and nisin resistance were also increased. Transcriptome analysis showed that nisin immunity and the biosynthesis of some amino acids, pyrimidine, and exopolysaccharides were enhanced in the engineered strain. This study elucidates the regulation mechanism of YthA and provides a novel strategy for constructing robust industrial L. lactis strains.
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Contribution of YthA, a PspC Family Transcriptional Regulator of Lactococcus lactis F44 Acid Tolerance and Nisin Yield: a Transcriptomic Approach. Appl Environ Microbiol 2018; 84:AEM.02483-17. [PMID: 29305506 DOI: 10.1128/aem.02483-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/22/2017] [Indexed: 11/20/2022] Open
Abstract
To overcome the adverse impacts of environmental stresses during growth, different adaptive regulation mechanisms can be activated in Lactococcus lactis In this study, the transcription levels of eight transcriptional regulators of L. lactis subsp. lactis F44 under acid stress were analyzed using quantitative reverse transcription-PCR. Eight gene-overexpressing strains were then constructed to examine their influences on acid-resistant capability. Overexpressing ythA, a PspC family transcriptional regulator, increased the survival rate by 3.2-fold compared to the control at the lethal pH 3.0 acid shock. Moreover, the nisin yield was increased by 45.50%. The ythA-overexpressing strain FythA appeared to have higher intracellular pH stability and nisin-resistant ability. Subsequently, transcriptome analysis revealed that the vast majority of genes associated with amino acid biosynthesis, including arginine, serine, phenylalanine, and tyrosine, were predominantly upregulated in FythA. Arginine biosynthesis (argG and argH), arginine deiminase pathway, and polar amino acid transport (ysfE and ysfF) were proposed to be the main regulation mechanisms of YthA. Furthermore, the transcription of genes associated with pyrimidine and exopolysaccharide biosynthesis were upregulated. The transcriptional levels of nisIPRKFEG genes were substantially higher in FythA, which directly contributed to the yield and resistance of nisin. Three potential DNA-binding sequences were predicted by computer analysis using the upstream regions of genes with prominent changes. This study showed that YthA could increase acid resistance and nisin yield and revealed a putative regulation mechanism of YthA.IMPORTANCE Nisin, produced by Lactococcus lactis subsp. lactis, is widely used as a safe food preservative. Acid stress becomes the primary restrictive factor of cell growth and nisin yield. In this research, we found that the transcriptional regulator YthA was conducive to enhancing the acid resistance of L. lactis F44. Overexpressing ythA could significantly improve the survival rate and nisin yield. The stability of intracellular pH and nisin resistance were also increased. Transcriptome analysis showed that nisin immunity and the biosynthesis of some amino acids, pyrimidine, and exopolysaccharides were enhanced in the engineered strain. This study elucidates the regulation mechanism of YthA and provides a novel strategy for constructing robust industrial L. lactis strains.
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The spatiotemporal system dynamics of acquired resistance in an engineered microecology. Sci Rep 2017; 7:16071. [PMID: 29167517 PMCID: PMC5700104 DOI: 10.1038/s41598-017-16176-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/08/2017] [Indexed: 12/24/2022] Open
Abstract
Great strides have been made in the understanding of complex networks; however, our understanding of natural microecologies is limited. Modelling of complex natural ecological systems has allowed for new findings, but these models typically ignore the constant evolution of species. Due to the complexity of natural systems, unanticipated interactions may lead to erroneous conclusions concerning the role of specific molecular components. To address this, we use a synthetic system to understand the spatiotemporal dynamics of growth and to study acquired resistance in vivo. Our system differs from earlier synthetic systems in that it focuses on the evolution of a microecology from a killer-prey relationship to coexistence using two different non-motile Escherichia coli strains. Using empirical data, we developed the first ecological model emphasising the concept of the constant evolution of species, where the survival of the prey species is dependent on location (distance from the killer) or the evolution of resistance. Our simple model, when expanded to complex microecological association studies under varied spatial and nutrient backgrounds may help to understand the complex relationships between multiple species in intricate natural ecological networks. This type of microecological study has become increasingly important, especially with the emergence of antibiotic-resistant pathogens.
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Silva KPT, Chellamuthu P, Boedicker JQ. Quantifying the strength of quorum sensing crosstalk within microbial communities. PLoS Comput Biol 2017; 13:e1005809. [PMID: 29049387 PMCID: PMC5663516 DOI: 10.1371/journal.pcbi.1005809] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 10/31/2017] [Accepted: 10/05/2017] [Indexed: 01/12/2023] Open
Abstract
In multispecies microbial communities, the exchange of signals such as acyl-homoserine lactones (AHL) enables communication within and between species of Gram-negative bacteria. This process, commonly known as quorum sensing, aids in the regulation of genes crucial for the survival of species within heterogeneous populations of microbes. Although signal exchange was studied extensively in well-mixed environments, less is known about the consequences of crosstalk in spatially distributed mixtures of species. Here, signaling dynamics were measured in a spatially distributed system containing multiple strains utilizing homologous signaling systems. Crosstalk between strains containing the lux, las and rhl AHL-receptor circuits was quantified. In a distributed population of microbes, the impact of community composition on spatio-temporal dynamics was characterized and compared to simulation results using a modified reaction-diffusion model. After introducing a single term to account for crosstalk between each pair of signals, the model was able to reproduce the activation patterns observed in experiments. We quantified the robustness of signal propagation in the presence of interacting signals, finding that signaling dynamics are largely robust to interference. The ability of several wild isolates to participate in AHL-mediated signaling was investigated, revealing distinct signatures of crosstalk for each species. Our results present a route to characterize crosstalk between species and predict systems-level signaling dynamics in multispecies communities.
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Affiliation(s)
- Kalinga Pavan T. Silva
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, United States of America
| | - Prithiviraj Chellamuthu
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, United States of America
| | - James Q. Boedicker
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, United States of America
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
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Scholes NS, Isalan M. A three-step framework for programming pattern formation. Curr Opin Chem Biol 2017; 40:1-7. [DOI: 10.1016/j.cbpa.2017.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/24/2017] [Accepted: 04/10/2017] [Indexed: 12/31/2022]
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Jiang Y, Yang G, Wang Q, Wang Z, Yang W, Gu W, Shi C, Wang J, Huang H, Wang C. Molecular mechanisms underlying protection against H9N2 influenza virus challenge in mice by recombinant Lactobacillus plantarum with surface displayed HA2-LTB. J Biotechnol 2017; 259:6-14. [PMID: 28811215 DOI: 10.1016/j.jbiotec.2017.08.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/24/2017] [Accepted: 08/09/2017] [Indexed: 12/29/2022]
Abstract
It has been considered that the Avian influenza virus (AIV) causes severe threats to poultry industry. In this study, we constructed a series of recombinant Lactobacillus plantarum (L. plantarum) with surface displayed hemagglutinin subunit 2 (HA2) alone or together with heat-labile toxin B subunit (LTB) from enterotoxigenic Escherichia coli. Balb/c mice were used as model to evaluate the protective effects of recombinant L. plantarum strains against H9N2 subtype challenge. The results showed that the presence of LTB significantly increased the percentages of CD3+CD4+IL-4+, CD3+CD4+IFN-γ+ and CD3+CD4+IL-17+ T cells, as well as CD3+CD8+IFN-γ+ T cells in spleen and MLNs determined by Fluorescence-Activated Cell Sorting assay. Similar increased production of serum IFN-γ was also confirmed by enzyme linked immunosorbent assay (ELISA). The L. plantarum with surface displayed HA2-LTB also dramatically increased the percentages of B220+ IgA+ B cells in peyer patch, in consistent with elevated production of mucosal SIgA antibody determined by ELISA. Finally, the orally administrated HA2-LTB expressing strain efficiently protected mice against H9N2 subtype AIV challenge shown by increased survival percentages, body weight gains and decreased lung lesions in histopathologic analysis. In conclusion, this study provides more detail mechanisms underlying the adjuvant effects of LTB on heterologous antigen produced in recombinant lactic acid bacteria.
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Affiliation(s)
- Yanlong Jiang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Guilian Yang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Qi Wang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Zhannan Wang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Wentao Yang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Wei Gu
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China; Shandong Baolai-Leelai Bio-Tech Co., LTD, Taian, Shandong Province, 171000, China
| | - Chunwei Shi
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Jianzhong Wang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Haibin Huang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Chunfeng Wang
- College of Animal Science and Technology, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China.
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Silva KP, Chellamuthu P, Boedicker JQ. Signal Destruction Tunes the Zone of Activation in Spatially Distributed Signaling Networks. Biophys J 2017; 112:1037-1044. [PMID: 28297640 DOI: 10.1016/j.bpj.2017.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 01/03/2017] [Accepted: 01/10/2017] [Indexed: 12/12/2022] Open
Abstract
Diverse microbial communities coordinate group behaviors through signal exchange, such as the exchange of acyl-homoserine lactones (AHLs) by Gram-negative bacteria. Cellular communication is prone to interference by neighboring microbes. One mechanism of interference is signal destruction through the production of an enzyme that cleaves the signaling molecule. Here we examine the ability of one such interference enzyme, AiiA, to modulate signal propagation in a spatially distributed system of bacteria. We have developed an experimental assay to measure signal transduction and implement a theoretical model of signaling dynamics to predict how the system responds to interference. We show that titration of an interfering strain into a signaling network tunes the spatial range of activation over the centimeter length scale, quantifying the robustness of the signaling network to signal destruction and demonstrating the ability to program systems-level responses of spatially heterogeneous cellular networks.
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Affiliation(s)
- Kalinga Pavan Silva
- Department of Physics, University of Southern California, Los Angeles, California
| | - Prithiviraj Chellamuthu
- Department of Physics, University of Southern California, Los Angeles, California; Department of Biological Sciences, University of Southern California, Los Angeles, California
| | - James Q Boedicker
- Department of Physics, University of Southern California, Los Angeles, California; Department of Biological Sciences, University of Southern California, Los Angeles, California.
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Promoting acid resistance and nisin yield of Lactococcus lactis F44 by genetically increasing D-Asp amidation level inside cell wall. Appl Microbiol Biotechnol 2017. [PMID: 28643181 DOI: 10.1007/s00253-017-8365-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nisin fermentation by Lactococcus lactis requires a low pH to maintain a relatively higher nisin activity. However, the acidic environment will result in cell arrest, and eventually decrease the relative nisin production. Hence, constructing an acid-resistant L. lactis is crucial for nisin harvest in acidic nisin fermentation. In this paper, the first discovery of the relationship between D-Asp amidation-associated gene (asnH) and acid resistance was reported. Overexpression of asnH in L. lactis F44 (F44A) resulted in a sevenfold increase in survival capacity during acid shift (pH 3) and enhanced nisin desorption capacity compared to F44 (wild type), which subsequently contributed to higher nisin production, reaching 5346 IU/mL, 57.0% more than that of F44 in the fed-batch fermentation. Furthermore, the engineered F44A showed a moderate increase in D-Asp amidation level (from 82 to 92%) compared to F44. The concomitant decrease of the negative charge inside the cell wall was detected by a newly developed method based on the nisin adsorption amount onto cell surface. Meanwhile, peptidoglycan cross-linkage increased from 36.8% (F44) to 41.9% (F44A), and intracellular pH can be better maintained by blocking extracellular H+ due to the maintenance of peptidoglycan integrity, which probably resulted from the action of inhibiting hydrolases activity. The inference was further supported by the acmC-overexpression strain F44C, which was characterized by uncontrolled peptidoglycan hydrolase activity. Our results provided a novel strategy for enhancing nisin yield through cell wall remodeling, which contributed to both continuous nisin synthesis and less nisin adsorption in acidic fermentation (dual enhancement).
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