1
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Song HS, Lee NR, Kessell AK, McCullough HC, Park SY, Zhou K, Lee DY. Kinetics-based inference of environment-dependent microbial interactions and their dynamic variation. mSystems 2024; 9:e0130523. [PMID: 38682902 PMCID: PMC11097648 DOI: 10.1128/msystems.01305-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/28/2024] [Indexed: 05/01/2024] Open
Abstract
Microbial communities in nature are dynamically evolving as member species change their interactions subject to environmental variations. Accounting for such context-dependent dynamic variations in interspecies interactions is critical for predictive ecological modeling. In the absence of generalizable theoretical foundations, we lack a fundamental understanding of how microbial interactions are driven by environmental factors, significantly limiting our capability to predict and engineer community dynamics and function. To address this issue, we propose a novel theoretical framework that allows us to represent interspecies interactions as an explicit function of environmental variables (such as substrate concentrations) by combining growth kinetics and a generalized Lotka-Volterra model. A synergistic integration of these two complementary models leads to the prediction of alterations in interspecies interactions as the outcome of dynamic balances between positive and negative influences of microbial species in mixed relationships. The effectiveness of our method was experimentally demonstrated using a synthetic consortium of two Escherichia coli mutants that are metabolically dependent (due to an inability to synthesize essential amino acids) but competitively grow on a shared substrate. The analysis of the E. coli binary consortium using our model not only showed how interactions between the two amino acid auxotrophic mutants are controlled by the dynamic shifts in limiting substrates but also enabled quantifying previously uncharacterizable complex aspects of microbial interactions, such as asymmetry in interactions. Our approach can be extended to other ecological systems to model their environment-dependent interspecies interactions from growth kinetics.IMPORTANCEModeling environment-controlled interspecies interactions through separate identification of positive and negative influences of microbes in mixed relationships is a new capability that can significantly improve our ability to understand, predict, and engineer the complex dynamics of microbial communities. Moreover, the prediction of microbial interactions as a function of environmental variables can serve as valuable benchmark data to validate modeling and network inference tools in microbial ecology, the development of which has often been impeded due to the lack of ground truth information on interactions. While demonstrated against microbial data, the theory developed in this work is readily applicable to general community ecology to predict interactions among macroorganisms, such as plants and animals, as well as microorganisms.
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Affiliation(s)
- Hyun-Seob Song
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Na-Rae Lee
- Research Institute for Bioactive-Metabolome Network, Konkuk University, Seoul, South Korea
| | - Aimee K. Kessell
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Hugh C. McCullough
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Seo-Young Park
- School of Chemical Engineering, Sungkyunkwan University, Suwon-si, Gyeonggi-do, South Korea
| | - Kang Zhou
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, Suwon-si, Gyeonggi-do, South Korea
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2
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Liu Y, Xue B, Liu H, Wang S, Su H. Rational construction of synthetic consortia: Key considerations and model-based methods for guiding the development of a novel biosynthesis platform. Biotechnol Adv 2024; 72:108348. [PMID: 38531490 DOI: 10.1016/j.biotechadv.2024.108348] [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: 02/04/2024] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
The rapid development of synthetic biology has significantly improved the capabilities of mono-culture systems in converting different substrates into various value-added bio-chemicals through metabolic engineering. However, overexpression of biosynthetic pathways in recombinant strains can impose a heavy metabolic burden on the host, resulting in imbalanced energy distribution and negatively affecting both cell growth and biosynthesis capacity. Synthetic consortia, consisting of two or more microbial species or strains with complementary functions, have emerged as a promising and efficient platform to alleviate the metabolic burden and increase product yield. However, research on synthetic consortia is still in its infancy, with numerous challenges regarding the design and construction of stable synthetic consortia. This review provides a comprehensive comparison of the advantages and disadvantages of mono-culture systems and synthetic consortia. Key considerations for engineering synthetic consortia based on recent advances are summarized, and simulation and computational tools for guiding the advancement of synthetic consortia are discussed. Moreover, further development of more efficient and cost-effective synthetic consortia with emerging technologies such as artificial intelligence and machine learning is highlighted.
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Affiliation(s)
- Yu Liu
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Boyuan Xue
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Hao Liu
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Shaojie Wang
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China.
| | - Haijia Su
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China.
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3
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Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted CN, Majumder ELW, Kumar D, Awasthi D, Mukhopadhyay A, Singer SW, Gladden JM, Simmons BA, Choudhary H. Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries. CHEMSUSCHEM 2024:e202301460. [PMID: 38669480 DOI: 10.1002/cssc.202301460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shubhasish Goswami
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Valentina Garcia
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Elizabeth Zhou
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
| | - Charles N Olmsted
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA 94550, United States
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4
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Huang BD, Kim D, Yu Y, Wilson CJ. Engineering intelligent chassis cells via recombinase-based MEMORY circuits. Nat Commun 2024; 15:2418. [PMID: 38499601 PMCID: PMC10948884 DOI: 10.1038/s41467-024-46755-1] [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: 10/16/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024] Open
Abstract
Synthetic biologists seek to engineer intelligent living systems capable of decision-making, communication, and memory. Separate technologies exist for each tenet of intelligence; however, the unification of all three properties in a living system has not been achieved. Here, we engineer completely intelligent Escherichia coli strains that harbor six orthogonal and inducible genome-integrated recombinases, forming Molecularly Encoded Memory via an Orthogonal Recombinase arraY (MEMORY). MEMORY chassis cells facilitate intelligence via the discrete multi-input regulation of recombinase functions enabling inheritable DNA inversions, deletions, and genomic insertions. MEMORY cells can achieve programmable and permanent gain (or loss) of functions extrachromosomally or from a specific genomic locus, without the loss or modification of the MEMORY platform - enabling the sequential programming and reprogramming of DNA circuits within the cell. We demonstrate all three tenets of intelligence via a probiotic (Nissle 1917) MEMORY strain capable of information exchange with the gastrointestinal commensal Bacteroides thetaiotaomicron.
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Affiliation(s)
- Brian D Huang
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, 311 Ferst Drive, Atlanta, GA, 30332-0100, Georgia
| | - Dowan Kim
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, 311 Ferst Drive, Atlanta, GA, 30332-0100, Georgia
| | - Yongjoon Yu
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, 311 Ferst Drive, Atlanta, GA, 30332-0100, Georgia
| | - Corey J Wilson
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, 311 Ferst Drive, Atlanta, GA, 30332-0100, Georgia.
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5
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Buson F, Gao Y, Wang B. Genetic Parts and Enabling Tools for Biocircuit Design. ACS Synth Biol 2024; 13:697-713. [PMID: 38427821 DOI: 10.1021/acssynbio.3c00691] [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] [Indexed: 03/03/2024]
Abstract
Synthetic biology aims to engineer biological systems for customized tasks through the bottom-up assembly of fundamental building blocks, which requires high-quality libraries of reliable, modular, and standardized genetic parts. To establish sets of parts that work well together, synthetic biologists created standardized part libraries in which every component is analyzed in the same metrics and context. Here we present a state-of-the-art review of the currently available part libraries for designing biocircuits and their gene expression regulation paradigms at transcriptional, translational, and post-translational levels in Escherichia coli. We discuss the necessary facets to integrate these parts into complex devices and systems along with the current efforts to catalogue and standardize measurement data. To better display the range of available parts and to facilitate part selection in synthetic biology workflows, we established biopartsDB, a curated database of well-characterized and useful genetic part and device libraries with detailed quantitative data validated by the published literature.
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Affiliation(s)
- Felipe Buson
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
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6
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Zhang Q, Wang Q, Chen H, Chen L, Wang F, Gu Z, Shi G, Liu L, Ding Z. Lignin-degrading enzyme production was enhanced by the novel transcription factor Ptf6 in synergistic microbial co-culture. Microbiol Res 2024; 280:127575. [PMID: 38147744 DOI: 10.1016/j.micres.2023.127575] [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: 09/12/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/28/2023]
Abstract
Synergistic microbial co-culture has been an efficient and energy-saving strategy to produce lignin-degrading enzymes (LDEs), including laccase, manganese peroxidase, and versatile peroxidase. However, the regulatory mechanism of microbial co-culture is still unclear. Herein, the extracellular LDE activities of four white-rot fungi were significantly increased by 88-544% over monoculture levels when co-cultured with Rhodotorula mucilaginosa. Ptf6 was demonstrated from the 9 million Y1H clone library to be a shared GATA transcription factor in the four fungi, and could directly bind to the laccase gene promoter. Ptf6 exists in two alternatively spliced isoforms under monoculture, namely Ptf6-α (1078 amino acids) containing Cys2/Cys2-type zinc finger and Ptf6-β (963 amino acids) lacking the complete domain. Ptf6 responded to co-culture by up-regulation of both its own transcripts and the proportion of Ptf6-α. Ptf6-α positively activated the production of most LDE isoenzymes and bound to four GATA motifs on the LDEs' promoter with different affinities. Moreover, Ptf6-regulation mechanism can be applicable to a variety of microbial co-culture systems. This study lays a theoretical foundation for further improving LDEs production and providing an efficient way to enhance the effects of biological and enzymatic pretreatment for lignocellulosic biomass conversion.
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Affiliation(s)
- Qi Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Qiong Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Haixiu Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Lei Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Feng Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Zhenghua Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Guiyang Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhongyang Ding
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China.
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7
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Zeng M, Sarker B, Rondthaler SN, Vu V, Andrews LB. Identifying LasR Quorum Sensors with Improved Signal Specificity by Mapping the Sequence-Function Landscape. ACS Synth Biol 2024; 13:568-589. [PMID: 38206199 DOI: 10.1021/acssynbio.3c00543] [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] [Indexed: 01/12/2024]
Abstract
Programmable intercellular signaling using components of naturally occurring quorum sensing can allow for coordinated functions to be engineered in microbial consortia. LuxR-type transcriptional regulators are widely used for this purpose and are activated by homoserine lactone (HSL) signals. However, they often suffer from imperfect molecular discrimination of structurally similar HSLs, causing misregulation within engineered consortia containing multiple HSL signals. Here, we studied one such example, the regulator LasR from Pseudomonas aeruginosa. We elucidated its sequence-function relationship for ligand specificity using targeted protein engineering and multiplexed high-throughput biosensor screening. A pooled combinatorial saturation mutagenesis library (9,486 LasR DNA sequences) was created by mutating six residues in LasR's β5 sheet with single, double, or triple amino acid substitutions. Sort-seq assays were performed in parallel using cognate and noncognate HSLs to quantify each corresponding sensor's response to each HSL signal, which identified hundreds of highly specific variants. Sensor variants identified were individually assayed and exhibited up to 60.6-fold (p = 0.0013) improved relative activation by the cognate signal compared to the wildtype. Interestingly, we uncovered prevalent mutational epistasis and previously unidentified residues contributing to signal specificity. The resulting sensors with negligible signal crosstalk could be broadly applied to engineer bacteria consortia.
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Affiliation(s)
- Min Zeng
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Biprodev Sarker
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Stephen N Rondthaler
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Vanessa Vu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B Andrews
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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8
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Darvishi F, Rafatiyan S, Abbaspour Motlagh Moghaddam MH, Atkinson E, Ledesma-Amaro R. Applications of synthetic yeast consortia for the production of native and non-native chemicals. Crit Rev Biotechnol 2024; 44:15-30. [PMID: 36130800 DOI: 10.1080/07388551.2022.2118569] [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: 06/03/2022] [Revised: 08/03/2022] [Accepted: 08/19/2022] [Indexed: 11/03/2022]
Abstract
The application of microbial consortia is a new approach in synthetic biology. Synthetic yeast consortia, simple or complex synthetic mixed cultures, have been used for the production of various metabolites. Cooperation between the members of a consortium and cross-feeding can be applied to create stable microbial communication. These consortia can: consume a variety of substrates, perform more complex functions, produce metabolites in high titer, rate, and yield (TRY), and show higher stability during industrial fermentations. Due to the new research context of synthetic consortia, few yeasts were used to build these consortia, including Saccharomyces cerevisiae, Pichia pastoris, and Yarrowia lipolytica. Here, application of the yeasts for design of synthetic microbial consortia and their advantages and bottlenecks for effective and robust production of valuable metabolites from bioresource, including: cellulose, xylose, glycerol and so on, have been reviewed. Key trends and challenges are also discussed for the future development of synthetic yeast consortia.
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Affiliation(s)
- Farshad Darvishi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
- Research Center for Applied Microbiology and Microbial Biotechnology (CAMB), Alzahra University, Tehran, Iran
| | - Sajad Rafatiyan
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | | | - Eliza Atkinson
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
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9
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Zeng M, Sarker B, Howitz N, Shah I, Andrews LB. Synthetic Homoserine Lactone Sensors for Gram-Positive Bacillus subtilis Using LuxR-Type Regulators. ACS Synth Biol 2024; 13:282-299. [PMID: 38079538 PMCID: PMC10805106 DOI: 10.1021/acssynbio.3c00504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 01/23/2024]
Abstract
A universal biochemical signal for bacterial cell-cell communication could facilitate programming dynamic responses in diverse bacterial consortia. However, the classical quorum sensing paradigm is that Gram-negative and Gram-positive bacteria generally communicate via homoserine lactones (HSLs) or oligopeptide molecular signals, respectively, to elicit population responses. Here, we create synthetic HSL sensors for Gram-positive Bacillus subtilis 168 using allosteric LuxR-type regulators (RpaR, LuxR, RhlR, and CinR) and synthetic promoters. Promoters were combinatorially designed from different sequence elements (-35, -16, -10, and transcriptional start regions). We quantified the effects of these combinatorial promoters on sensor activity and determined how regulator expression affects its activation, achieving up to 293-fold activation. Using the statistical design of experiments, we identified significant effects of promoter regions and pairwise interactions on sensor activity, which helped to understand the sequence-function relationships for synthetic promoter design. We present the first known set of functional HSL sensors (≥20-fold dynamic range) in B. subtilis for four different HSL chemical signals: p-coumaroyl-HSL, 3-oxohexanoyl-HSL, n-butyryl-HSL, and n-(3-hydroxytetradecanoyl)-HSL. This set of synthetic HSL sensors for a Gram-positive bacterium can pave the way for designable interspecies communication within microbial consortia.
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Affiliation(s)
- Min Zeng
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Biprodev Sarker
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Nathaniel Howitz
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Ishita Shah
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B. Andrews
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Molecular
and Cellular Biology Graduate Program, University
of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology
Training Program, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
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10
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Jonkergouw C, Savola P, Osmekhina E, van Strien J, Batys P, Linder MB. Exploration of Chemical Diversity in Intercellular Quorum Sensing Signalling Systems in Prokaryotes. Angew Chem Int Ed Engl 2024; 63:e202314469. [PMID: 37877232 DOI: 10.1002/anie.202314469] [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: 09/26/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 10/26/2023]
Abstract
Quorum sensing (QS) serves as a vital means of intercellular signalling in a variety of prokaryotes, which enables single cells to act in multicellular configurations. The potential to control community-wide responses has also sparked numerous recent biotechnological innovations. However, our capacity to utilize intercellular communication is hindered due to a scarcity of complementary signalling systems and a restricted comprehension of interconnections between these systems caused by variations in their dynamic range. In this study, we utilize uniform manifold approximation and projection and extended-connectivity fingerprints to explore the available chemical space of QS signalling molecules. We investigate and experimentally characterize a set of closely related QS signalling ligands, consisting of N-acyl homoserine lactones and the aryl homoserine lactone p-coumaroyl, as well as a set of more widely diverging QS ligands, consisting of photopyrones, dialkylresorcinols, 3,5-dimethylpyrazin-2-ol and autoinducer-2, and define their performance. We report on a set of six signal- and promoter-orthogonal intercellular QS signalling systems, significantly expanding the toolkit for engineering community-wide behaviour. Furthermore, we demonstrate that ligand diversity can serve as a statistically significant tool to predict much more complicated ligand-receptor interactions. This approach highlights the potential of dimensionality reduction to explore chemical diversity in microbial dynamics.
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Affiliation(s)
- Christopher Jonkergouw
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Pihla Savola
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Ekaterina Osmekhina
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Joeri van Strien
- Medical BioSciences Department, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Piotr Batys
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30239, Krakow, Poland
| | - Markus B Linder
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
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11
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Xi C, Diao J, Moon TS. Advances in ligand-specific biosensing for structurally similar molecules. Cell Syst 2023; 14:1024-1043. [PMID: 38128482 PMCID: PMC10751988 DOI: 10.1016/j.cels.2023.10.009] [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: 05/21/2023] [Revised: 08/23/2023] [Accepted: 10/19/2023] [Indexed: 12/23/2023]
Abstract
The specificity of biological systems makes it possible to develop biosensors targeting specific metabolites, toxins, and pollutants in complex medical or environmental samples without interference from structurally similar compounds. For the last two decades, great efforts have been devoted to creating proteins or nucleic acids with novel properties through synthetic biology strategies. Beyond augmenting biocatalytic activity, expanding target substrate scopes, and enhancing enzymes' enantioselectivity and stability, an increasing research area is the enhancement of molecular specificity for genetically encoded biosensors. Here, we summarize recent advances in the development of highly specific biosensor systems and their essential applications. First, we describe the rational design principles required to create libraries containing potential mutants with less promiscuity or better specificity. Next, we review the emerging high-throughput screening techniques to engineer biosensing specificity for the desired target. Finally, we examine the computer-aided evaluation and prediction methods to facilitate the construction of ligand-specific biosensors.
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Affiliation(s)
- Chenggang Xi
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Jinjin Diao
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA.
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12
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Jin X, Gao Y, Chen X, Wang S, Qi Q, Liang Q. The Construction of the Self-Induced Sal System and Its Application in Salicylic Acid Production. Molecules 2023; 28:7825. [PMID: 38067556 PMCID: PMC10708014 DOI: 10.3390/molecules28237825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The design and construction of more complex and delicate genetic control circuits suffer from poor orthogonality in quorum sensing (QS) systems. The Sal system, which relies on salicylic acid as a signaling molecule, is an artificially engineered regulatory system with a structure that differs significantly from that of natural QS signaling molecules. Salicylic acid is an important drug precursor, mainly used in the production of drugs such as aspirin and anti-HIV drugs. However, there have been no reports on the construction of a self-induced Sal system in single cells. In this study, a high-copy plasmid backbone was used to construct the regulatory proteins and a self-induced promoter of salicylic acid in E. coli by adjusting the precise regulation of key gene expression; the sensitivity and induction range of this system were improved. Subsequently, the exogenous gene pchBA was introduced in E. coli to extend the shikimate pathway and synthesize salicylic acid, resulting in the construction of the first complete self-induced Sal system. Finally, the self-induced Sal System was combined with artificial trans-encoded sRNAs (atsRNAs) to repress the growth-essential gene ppc and accumulate the precursor substance PEP, thereby increasing the titer of salicylic acid by 151%. This construction of a self-induced artificial system introduces a new tool for selecting communication tools and induction systems in synthetic biology and metabolic engineering, but also demonstrates a self-inducible pathway design strategy for salicylic acid biosynthesis.
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Affiliation(s)
| | | | | | | | | | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (X.J.); (Y.G.); (X.C.); (S.W.); (Q.Q.)
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13
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Jiang Y, Wu R, Zhang W, Xin F, Jiang M. Construction of stable microbial consortia for effective biochemical synthesis. Trends Biotechnol 2023; 41:1430-1441. [PMID: 37330325 DOI: 10.1016/j.tibtech.2023.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 06/19/2023]
Abstract
Microbial consortia can complete otherwise arduous tasks through the cooperation of multiple microbial species. This concept has been applied to produce commodity chemicals, natural products, and biofuels. However, metabolite incompatibility and growth competition can make the microbial composition unstable, and fluctuating microbial populations reduce the efficiency of chemical production. Thus, controlling the populations and regulating the complex interactions between different strains are challenges in constructing stable microbial consortia. This Review discusses advances in synthetic biology and metabolic engineering to control social interactions within microbial cocultures, including substrate separation, byproduct elimination, crossfeeding, and quorum-sensing circuit design. Additionally, this Review addresses interdisciplinary strategies to improve the stability of microbial consortia and provides design principles for microbial consortia to enhance chemical production.
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Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China.
| | - Ruofan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China
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14
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Simpson K, L'Homme A, Keymer J, Federici F. Spatial biology of Ising-like synthetic genetic networks. BMC Biol 2023; 21:185. [PMID: 37667283 PMCID: PMC10478219 DOI: 10.1186/s12915-023-01681-4] [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: 12/20/2022] [Accepted: 08/11/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Understanding how spatial patterns of gene expression emerge from the interaction of individual gene networks is a fundamental challenge in biology. Developing a synthetic experimental system with a common theoretical framework that captures the emergence of short- and long-range spatial correlations (and anti-correlations) from interacting gene networks could serve to uncover generic scaling properties of these ubiquitous phenomena. RESULTS Here, we combine synthetic biology, statistical mechanics models, and computational simulations to study the spatial behavior of synthetic gene networks (SGNs) in Escherichia coli quasi-2D colonies growing on hard agar surfaces. Guided by the combined mechanisms of the contact process lattice simulation and two-dimensional Ising model (CPIM), we describe the spatial behavior of bi-stable and chemically coupled SGNs that self-organize into patterns of long-range correlations with power-law scaling or short-range anti-correlations. These patterns, resembling ferromagnetic and anti-ferromagnetic configurations of the Ising model near critical points, maintain their scaling properties upon changes in growth rate and cell shape. CONCLUSIONS Our findings shed light on the spatial biology of coupled and bistable gene networks in growing cell populations. This emergent spatial behavior could provide insights into the study and engineering of self-organizing gene patterns in eukaryotic tissues and bacterial consortia.
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Affiliation(s)
- Kevin Simpson
- ANID - Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Alfredo L'Homme
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan Keymer
- Institute for Advanced Studies, Shenzhen X-Institute, Shenzhen, China.
- Schools of Physics and Biology, Pontificia Universidad Católica de Chile, Santiago, Chile.
- Department of Natural Sciences and Technology, Universidad de Aysén, Coyhaique, Chile.
| | - Fernán Federici
- ANID - Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
- FONDAP Center for Genome Regulation - Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile.
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15
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Li C, Zheng H, Li H, Liu L, Wang J, Ni J. Synthetic Light-Driven Consortia for Carbon-Negative Biosynthesis. Chembiochem 2023; 24:e202300122. [PMID: 37401840 DOI: 10.1002/cbic.202300122] [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: 02/27/2023] [Revised: 05/07/2023] [Accepted: 07/03/2023] [Indexed: 07/05/2023]
Abstract
Synthetic light-driven consortia composed of phototrophs and heterotrophs have attracted increasing attention owing to their potential to be used in sustainable biotechnology. In recent years, synthetic phototrophic consortia have been used to produce bulk chemicals, biofuels, and other valuable bioproducts. In addition, autotrophic-heterotrophic symbiosis systems have potential applications in wastewater treatment, bioremediation, and as a method for phytoplankton bloom control. Here, we discuss progress made on the biosynthesis of phototrophic microbial consortia. In addition, strategies for optimizing the synthetic light-driven consortia are summarized. Moreover, we highlight current challenges and future research directions for the development of robust and controllable synthetic light-driven consortia.
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Affiliation(s)
- Chaofeng Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haotian Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hengrun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liangxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Ni
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
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16
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Smith JM, Hartmann D, Booth MJ. Engineering cellular communication between light-activated synthetic cells and bacteria. Nat Chem Biol 2023; 19:1138-1146. [PMID: 37414974 PMCID: PMC10449621 DOI: 10.1038/s41589-023-01374-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 05/30/2023] [Indexed: 07/08/2023]
Abstract
Gene-expressing compartments assembled from simple, modular parts, are a versatile platform for creating minimal synthetic cells with life-like functions. By incorporating gene regulatory motifs into their encapsulated DNA templates, in situ gene expression and, thereby, synthetic cell function can be controlled according to specific stimuli. In this work, cell-free protein synthesis within synthetic cells was controlled using light by encoding genes of interest on light-activated DNA templates. Light-activated DNA contained a photocleavable blockade within the T7 promoter region that tightly repressed transcription until the blocking groups were removed with ultraviolet light. In this way, synthetic cells were activated remotely, in a spatiotemporally controlled manner. By applying this strategy to the expression of an acyl homoserine lactone synthase, BjaI, quorum-sensing-based communication between synthetic cells and bacteria was controlled with light. This work provides a framework for the remote-controlled production and delivery of small molecules from nonliving matter to living matter, with applications in biology and medicine.
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Affiliation(s)
| | - Denis Hartmann
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Michael J Booth
- Department of Chemistry, University of Oxford, Oxford, UK.
- Department of Chemistry, University College London, London, UK.
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17
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Fu Y, Xu R, Yang B, Wu Y, Xia L, Tawfik A, Meng F. Mediation of Bacterial Interactions via a Novel Membrane-Based Segregator to Enhance Biological Nitrogen Removal. Appl Environ Microbiol 2023; 89:e0070923. [PMID: 37404187 PMCID: PMC10370321 DOI: 10.1128/aem.00709-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The regulation of microbial subpopulations in wastewater treatment plants (WWTPs) with desired functions can guarantee nutrient removal. In nature, "good fences make good neighbors," which can be applied to engineering microbial consortia. Herein, a membrane-based segregator (MBSR) was proposed, where porous membranes not only promote the diffusion of metabolic products but also isolate incompatible microbes. The MBSR was integrated with an anoxic/aerobic membrane bioreactor (i.e., an experimental MBR). The long-term operation showed that the experimental MBR exhibited higher nitrogen removal (10.45 ± 2.73 mg/L total nitrogen) than the control MBR (21.68 ± 4.23 mg/L) in the effluent. The MBSR resulted in much lower oxygen reduction potential in the anoxic tank of the experimental MBR (-82.00 mV) compared to that of the control MBR (83.25 mV). The lower oxygen reduction potential can inevitably aid in the occurrence of denitrification. The 16S rRNA sequencing showed that the MBSR significantly enriched acidogenic consortia, which yielded considerable volatile fatty acids by fermenting the added carbon sources and allowed efficient transfer of these small molecules to the denitrifying community. Moreover, the sludge communities of the experimental MBR harbored a higher abundance of denitrifying bacteria than those of the control MBR. Metagenomic analysis further corroborated these sequencing results. The spatially structured microbial communities in the experimental MBR system demonstrate the practicability of the MBSR, achieving nitrogen removal efficiency superior to that of mixed populations. Our study provides an engineering method for modulating the assembly and metabolic division of labor of subpopulations in WWTPs. IMPORTANCE This study provides an innovative and applicable method for regulating subpopulations (activated sludge and acidogenic consortia), which contributes to the precise control of the metabolic division of labor in biological wastewater treatment processes.
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Affiliation(s)
- Yue Fu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, PR China
| | - Ronghua Xu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, PR China
| | - Boyi Yang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, PR China
| | - Yingxin Wu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, PR China
| | - Lichao Xia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, PR China
| | - Ahmed Tawfik
- National Research Centre, Water Pollution Research Department, Dokki, Cairo, Egypt
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, PR China
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18
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Marken JP, Murray RM. Addressable and adaptable intercellular communication via DNA messaging. Nat Commun 2023; 14:2358. [PMID: 37095088 PMCID: PMC10126159 DOI: 10.1038/s41467-023-37788-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 03/31/2023] [Indexed: 04/26/2023] Open
Abstract
Engineered consortia are a major research focus for synthetic biologists because they can implement sophisticated behaviors inaccessible to single-strain systems. However, this functional capacity is constrained by their constituent strains' ability to engage in complex communication. DNA messaging, by enabling information-rich channel-decoupled communication, is a promising candidate architecture for implementing complex communication. But its major advantage, its messages' dynamic mutability, is still unexplored. We develop a framework for addressable and adaptable DNA messaging that leverages all three of these advantages and implement it using plasmid conjugation in E. coli. Our system can bias the transfer of messages to targeted receiver strains by 100- to 1000-fold, and their recipient lists can be dynamically updated in situ to control the flow of information through the population. This work lays the foundation for future developments that further utilize the unique advantages of DNA messaging to engineer previously-inaccessible levels of complexity into biological systems.
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Affiliation(s)
- John P Marken
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Richard M Murray
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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19
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Kokarakis E, Rillema R, Ducat DC, Sakkos JK. Developing Cyanobacterial Quorum Sensing Toolkits: Toward Interspecies Coordination in Mixed Autotroph/Heterotroph Communities. ACS Synth Biol 2022; 12:265-276. [PMID: 36573789 PMCID: PMC9872165 DOI: 10.1021/acssynbio.2c00527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
There has been substantial recent interest in the promise of sustainable, light-driven bioproduction using cyanobacteria, including developing efforts for microbial bioproduction using mixed autotroph/heterotroph communities, which could provide useful properties, such as division of metabolic labor. However, building stable mixed-species communities of sufficient productivity remains a challenge, partly due to the lack of strategies for synchronizing and coordinating biological activities across different species. To address this obstacle, we developed an inter-species communication system using quorum sensing (QS) modules derived from well-studied pathways in heterotrophic microbes. In the model cyanobacterium, Synechococcus elongatus PCC 7942 (S. elongatus), we designed, integrated, and characterized genetic circuits that detect acyl-homoserine lactones (AHLs), diffusible signals utilized in many QS pathways. We showed that these receiver modules sense exogenously supplied AHL molecules and activate gene expression in a dose-dependent manner. We characterized these AHL receiver circuits in parallel with Escherichia coli W (E. coli W) to dissect species-specific properties, finding broad agreement, albeit with increased basal expression in S. elongatus. Our engineered "sender" E. coli strains accumulated biologically synthesized AHLs within the supernatant and activated receiver strains similarly to exogenous AHL activation. Our results will bolster the design of sophisticated genetic circuits in cyanobacterial/heterotroph consortia and the engineering of QS-like behaviors across cyanobacterial populations.
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Affiliation(s)
- Emmanuel
J. Kokarakis
- Plant
Research Laboratory, Michigan State University, East Lansing, Michigan48824-1312, United States,Department
of Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan48824-1312, United States
| | - Rees Rillema
- Plant
Research Laboratory, Michigan State University, East Lansing, Michigan48824-1312, United States,Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan48824-1312, United States
| | - Daniel C. Ducat
- Plant
Research Laboratory, Michigan State University, East Lansing, Michigan48824-1312, United States,Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan48824-1312, United States
| | - Jonathan K. Sakkos
- Plant
Research Laboratory, Michigan State University, East Lansing, Michigan48824-1312, United States,
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20
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Deng T, Lin FC, Zink JI, Yu Q. Regulation of Bacterial Behavior by Light and Magnetism Mediated by Mesoporous Silica-Coated MnFe 2O 4@CoFe 2O 4 Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2022; 14:56007-56017. [PMID: 36509713 DOI: 10.1021/acsami.2c12589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Unicellular bacterial cells exhibit diverse population behaviors (i.e., aggregation, dispersion, directed assembly, biofilm formation, etc.) to facilitate communication and cooperation. Suitable bacterial behaviors are required for efficient nutrient uptake, cell recycling, and stress response for environmental and industrial application of bacterial populations. However, it remains a great challenge to artificially control bacterial behaviors because of complicated genetic and biochemical mechanisms. In this study, we designed facile mesoporous silica nanoparticle (MSN)-based assemblies to intelligently regulate bacterial behaviors with the help of light and magnetic field. This system was composed of magnetic MSNs, i.e., MnFe2O4@CoFe2O4@MSN modified by photoactive spiropyran (SP), and the chitosan-based polymers ChiPSP, i.e., chitosan grafted by triphenylphosphine and SP. The assembly strongly bound bacterial cells, inducing reversible bacterial aggregation by visible-light irradiation and dark. Moreover, the formed bacterial aggregates could be further governed by a directed magnetic field (DMF) to form microfibers and by an alternating magnetic field (AMF) to form biofilms. This study realized stimulus-triggered regulation of bacterial behaviors by MSNs and implied the great power of chemical strategies in intelligent control of diverse biological processes for environmental and industrial applications.
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Affiliation(s)
- Tian Deng
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Fang-Chu Lin
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jeffrey I Zink
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, P. R. China
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
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21
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Kang CW, Lim HG, Won J, Cha S, Shin G, Yang JS, Sung J, Jung GY. Circuit-guided population acclimation of a synthetic microbial consortium for improved biochemical production. Nat Commun 2022; 13:6506. [PMID: 36344561 PMCID: PMC9640620 DOI: 10.1038/s41467-022-34190-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
Microbial consortia have been considered potential platforms for bioprocessing applications. However, the complexity in process control owing to the use of multiple strains necessitates the use of an efficient population control strategy. Herein, we report circuit-guided synthetic acclimation as a strategy to improve biochemical production by a microbial consortium. We designed a consortium comprising alginate-utilizing Vibrio sp. dhg and 3-hydroxypropionic acid (3-HP)-producing Escherichia coli strains for the direct conversion of alginate to 3-HP. We introduced a genetic circuit, named "Population guider", in the E. coli strain, which degrades ampicillin only when 3-HP is produced. In the presence of ampicillin as a selection pressure, the consortium was successfully acclimated for increased 3-HP production by 4.3-fold compared to that by a simple co-culturing consortium during a 48-h fermentation. We believe this concept is a useful strategy for the development of robust consortium-based bioprocesses.
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Affiliation(s)
- Chae Won Kang
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Hyun Gyu Lim
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Jaehyuk Won
- grid.254224.70000 0001 0789 9563Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea ,grid.254224.70000 0001 0789 9563Department of Chemistry, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea
| | - Sanghak Cha
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Giyoung Shin
- grid.49100.3c0000 0001 0742 4007School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Jae-Seong Yang
- grid.423637.70000 0004 1763 5862Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193 Spain
| | - Jaeyoung Sung
- grid.254224.70000 0001 0789 9563Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea ,grid.254224.70000 0001 0789 9563Department of Chemistry, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea
| | - Gyoo Yeol Jung
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea ,grid.49100.3c0000 0001 0742 4007School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
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22
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Martinez JA, Delvenne M, Henrion L, Moreno F, Telek S, Dusny C, Delvigne F. Controlling microbial co-culture based on substrate pulsing can lead to stability through differential fitness advantages. PLoS Comput Biol 2022; 18:e1010674. [PMID: 36315576 PMCID: PMC9648842 DOI: 10.1371/journal.pcbi.1010674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/10/2022] [Accepted: 10/22/2022] [Indexed: 11/12/2022] Open
Abstract
Microbial consortia are an exciting alternative for increasing the performances of bioprocesses for the production of complex metabolic products. However, the functional properties of microbial communities remain challenging to control, considering the complex interaction mechanisms occurring between co-cultured microbial species. Indeed, microbial communities are highly dynamic and can adapt to changing environmental conditions through complex mechanisms, such as phenotypic diversification. We focused on stabilizing a co-culture of Saccharomyces cerevisiae and Escherichia coli in continuous cultures. Our preliminary data pointed out that transient diauxic shifts could lead to stable co-culture by providing periodic fitness advantages to the yeast. Based on a computational toolbox called MONCKS (for MONod-type Co-culture Kinetic Simulation), we were able to predict the dynamics of diauxic shift for both species based on a cybernetic approach. This toolbox was further used to predict the frequency of diauxic shift to be applied to reach co-culture stability. These simulations were successfully reproduced experimentally in continuous bioreactors with glucose pulsing. Finally, based on a bet-hedging reporter, we observed that the yeast population exhibited an increased phenotypic diversification process in co-culture compared with mono-culture, suggesting that this mechanism could be the basis of the metabolic fitness of the yeast. Being able to manipulate the dynamics of microbial co-cultures is a technical challenge that need to be addressed in order to get a deeper insight about how microbial communities are evolving in their ecological context, as well as for exploiting the potential offered by such communities in an applied context e.g., for setting up more robust bioprocesses relying on the use of several microbial species. In this study, we used continuous cultures of bacteria (E. coli) and yeast (S. cerevisiae) in order to demonstrate that a simple nutrient pulsing strategy can be used for adjusting the composition of the community with time. As expected, during growth on glucose, E. coli quickly outcompeted S. cerevisiae. However, when glucose is pulsed into the culture, increased metabolic fitness of the yeast was observed upon reconsumption of the main side metabolites i.e., acetate and ethanol, leading to a robust oscillating growth profile for both species. The optimal pulsing frequency was predicted based on a cybernetic version of a Monod growth model taking into account the main metabolic routes involved in the process. Considering the limited number of metabolic details needed, this cybernetic approach could be generalized to other communities.
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Affiliation(s)
- J. Andres Martinez
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Matheo Delvenne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Lucas Henrion
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Fabian Moreno
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Samuel Telek
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Christian Dusny
- Microscale Analysis and Engineering, Department of Solar Materials, Helmholtz-Centre for Environmental Research- UFZ Leipzig, Leipzig, Germany
| | - Frank Delvigne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
- * E-mail:
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23
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Chaos in synthetic microbial communities. PLoS Comput Biol 2022; 18:e1010548. [PMID: 36215322 PMCID: PMC9584520 DOI: 10.1371/journal.pcbi.1010548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 10/20/2022] [Accepted: 09/07/2022] [Indexed: 11/22/2022] Open
Abstract
Predictability is a fundamental requirement in biological engineering. As we move to building coordinated multicellular systems, the potential for such systems to display chaotic behaviour becomes a concern. Therefore understanding which systems show chaos is an important design consideration. We developed a methodology to explore the potential for chaotic dynamics in small microbial communities governed by resource competition, intercellular communication and competitive bacteriocin interactions. Our model selection pipeline uses Approximate Bayesian Computation to first identify oscillatory behaviours as a route to finding chaotic behaviour. We have shown that we can expect to find chaotic states in relatively small synthetic microbial systems, understand the governing dynamics and provide insights into how to control such systems. This work is the first to query the existence of chaotic behaviour in synthetic microbial communities and has important ramifications for the fields of biotechnology, bioprocessing and synthetic biology.
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24
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Lee TA, Steel H. Cybergenetic control of microbial community composition. Front Bioeng Biotechnol 2022; 10:957140. [PMID: 36277404 PMCID: PMC9582452 DOI: 10.3389/fbioe.2022.957140] [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: 05/30/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
The use of bacterial communities in bioproduction instead of monocultures has potential advantages including increased productivity through division of labour, ability to utilise cheaper substrates, and robustness against perturbations. A key challenge in the application of engineered bacterial communities is the ability to reliably control the composition of the community in terms of its constituent species. This is crucial to prevent faster growing species from outcompeting others with a lower relative fitness, and to ensure that all species are present at an optimal ratio during different steps in a biotechnological process. In contrast to purely biological approaches such as synthetic quorum sensing circuits or paired auxotrophies, cybergenetic control techniques - those in which computers interface with living cells-are emerging as an alternative approach with many advantages. The community composition is measured through methods such as fluorescence intensity or flow cytometry, with measured data fed real-time into a computer. A control action is computed using a variety of possible control algorithms and then applied to the system, with actuation taking the form of chemical (e.g., inducers, nutrients) or physical (e.g., optogenetic, mechanical) inputs. Subsequent changes in composition are then measured and the cycle repeated, maintaining or driving the system to a desired state. This review discusses recent and future developments in methods for implementing cybergenetic control systems, contrasts their capabilities with those of traditional biological methods of population control, and discusses future directions and outstanding challenges for the field.
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25
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Li L, Deng A, Liu S, Wang J, Shi R, Wang T, Cui D, Bai H, Zhang Y, Wen T. A Universal Method for Developing Autoinduction Expression Systems Using AHL-Mediated Quorum-Sensing Circuits. ACS Synth Biol 2022; 11:3114-3119. [PMID: 36000977 DOI: 10.1021/acssynbio.2c00400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A major challenge in engineering microorganisms for the desirable product is maintaining the rational balance between cell growth and production. Quorum sensing (QS)-based dynamic regulations provide a pathway-independent genetic control technology to rebalance metabolic flux for biomass and product synthesis. However, the lack of a universal method for screening QS elements and the complex design of autoinduction circuits limit their applications in metabolic engineering. Here, we developed a universal method for simple and rapid screening and evaluating various QS systems from Gram-negative bacteria, and the largest library containing 195 combinations of receiving device/signal molecules was constructed and evaluated in Escherichia coli. A simple logical circuit with different inducer synthesis rates was established to dynamically regulate gene expression levels, leading to efficient protein expression and product synthesis. The system was further applied in Pseudomonas putida, which indicated it could be widely accommodated in other microorganisms. Therefore, the method could be used in diverse Gram-negative strains for the desired biosynthesis.
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Affiliation(s)
- Lai Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Aihua Deng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,China Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100101, China
| | - Junyue Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Ruilin Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Tiantian Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Di Cui
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Bai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,China Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100101, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100101, China
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26
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Deter HS, Lu T. Engineering microbial consortia with rationally designed cellular interactions. Curr Opin Biotechnol 2022; 76:102730. [PMID: 35609504 PMCID: PMC10129393 DOI: 10.1016/j.copbio.2022.102730] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/22/2022] [Accepted: 04/03/2022] [Indexed: 12/14/2022]
Abstract
Synthetic microbial consortia represent a frontier of synthetic biology that promises versatile engineering of cellular functions. They are primarily developed through the design and construction of cellular interactions that coordinate individual dynamics and generate collective behaviors. Here we review recent advances in the engineering of synthetic communities through cellular-interaction programming. We first examine fundamental building blocks for intercellular communication and unidirectional positive and negative interactions. We then recap the assembly of the building blocks for creating bidirectional interactions in two-species ecosystems, which is followed by the discussion of engineering toward complex communities with increasing species numbers, under spatial contexts, and via model-guided design. We conclude by summarizing major challenges and future opportunities of engineered microbial ecosystems.
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Affiliation(s)
- Heather S Deter
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Intelligence Community Postdoctoral Research Fellowship Program, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA; Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA; National Center for Supercomputing Applications, Urbana, IL, USA.
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27
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Yin H, Chen Y, Feng Y, Feng L, Yu Q. Synthetic physical contact-remodeled rhizosphere microbiome for enhanced phytoremediation. JOURNAL OF HAZARDOUS MATERIALS 2022; 433:128828. [PMID: 35395523 DOI: 10.1016/j.jhazmat.2022.128828] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 03/21/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Phytoremediation is a prevalent strategy to treat environmental pollution caused by heavy metals and eutrophication-related pollutants. Although rhizosphere microbiome is critical for phytoremediation, it remains a great challenge to artificially remodel rhizosphere microbiome for enhancing multiple pollutant treatment. In this study, we designed a synthetic bacterium to strengthen physical contact between natural microbes and plant roots for remodeling the Eichhornia crassipes rhizosphere microbiome during phytoremediation. The synthetic bacterium EcCMC was constructed by introducing a surface-displayed synthetic protein CMC composed of two glucan-binding domains separated by the sequence of the fluorescent protein mCherry. This synthetic bacterium strongly bound glucans and recruited natural glucan-producing bacterial and fungal cells. Microbiome and metabolomic analysis revealed that EcCMC remarkably remodeled rhizosphere microbiome and increased stress response-related metabolites, leading to the increased activity of antioxidant enzymes involved in stress resistance. The remodeled microbiome further promoted plant growth, and enhanced accumulation of multiple pollutants into the plants, with the removal efficiency of the heavy metal cadmium, total organic matters, total nitrogen, total potassium, and total phosphorus reaching up to 98%, 80%, 97%, 93%, and 90%, respectively. This study sheds a novel light on remodeling of rhizosphere microbiome for enhanced phytoremediation of water and soil systems.
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Affiliation(s)
- Hongda Yin
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Yuqiao Chen
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Yuming Feng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Lian Feng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China.
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28
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Wang L, Zhang X, Tang C, Li P, Zhu R, Sun J, Zhang Y, Cui H, Ma J, Song X, Zhang W, Gao X, Luo X, You L, Chen Y, Dai Z. Engineering consortia by polymeric microbial swarmbots. Nat Commun 2022; 13:3879. [PMID: 35790722 PMCID: PMC9256712 DOI: 10.1038/s41467-022-31467-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/17/2022] [Indexed: 01/09/2023] Open
Abstract
Synthetic microbial consortia represent a new frontier for synthetic biology given that they can solve more complex problems than monocultures. However, most attempts to co-cultivate these artificial communities fail because of the winner-takes-all in nutrients competition. In soil, multiple species can coexist with a spatial organization. Inspired by nature, here we show that an engineered spatial segregation method can assemble stable consortia with both flexibility and precision. We create microbial swarmbot consortia (MSBC) by encapsulating subpopulations with polymeric microcapsules. The crosslinked structure of microcapsules fences microbes, but allows the transport of small molecules and proteins. MSBC method enables the assembly of various synthetic communities and the precise control over the subpopulations. These capabilities can readily modulate the division of labor and communication. Our work integrates the synthetic biology and material science to offer insights into consortia assembly and serve as foundation to diverse applications from biomanufacturing to engineered photosynthesis. Most attempts to co-cultivate the artificial microbial communities fail mostly due to the mismatched rates of consumption and production of nutrients among subpopulations. Here, the authors develop a microbial swarmbot mediated spatial segregation method to assemble stably coexisting consortia with both flexibility and precision.
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Affiliation(s)
- Lin Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xi Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chenwang Tang
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Pengcheng Li
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Runtao Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jing Sun
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yunfeng Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Hua Cui
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jiajia Ma
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Xinyu Song
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Xiang Gao
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaozhou Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Ye Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhuojun Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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29
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da Silva GAR, Oliveira SSDS, Lima SF, do Nascimento RP, Baptista ARDS, Fiaux SB. The industrial versatility of Gluconobacter oxydans: current applications and future perspectives. World J Microbiol Biotechnol 2022; 38:134. [PMID: 35688964 PMCID: PMC9187504 DOI: 10.1007/s11274-022-03310-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/13/2022] [Indexed: 11/26/2022]
Abstract
Gluconobacter oxydans is a well-known acetic acid bacterium that has long been applied in the biotechnological industry. Its extraordinary capacity to oxidize a variety of sugars, polyols, and alcohols into acids, aldehydes, and ketones is advantageous for the production of valuable compounds. Relevant G. oxydans industrial applications are in the manufacture of L-ascorbic acid (vitamin C), miglitol, gluconic acid and its derivatives, and dihydroxyacetone. Increasing efforts on improving these processes have been made in the last few years, especially by applying metabolic engineering. Thereby, a series of genes have been targeted to construct powerful recombinant strains to be used in optimized fermentation. Furthermore, low-cost feedstocks, mostly agro-industrial wastes or byproducts, have been investigated, to reduce processing costs and improve the sustainability of G. oxydans bioprocess. Nonetheless, further research is required mainly to make these raw materials feasible at the industrial scale. The current shortage of suitable genetic tools for metabolic engineering modifications in G. oxydans is another challenge to be overcome. This paper aims to give an overview of the most relevant industrial G. oxydans processes and the current strategies developed for their improvement.
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Affiliation(s)
- Gabrielle Alves Ribeiro da Silva
- Graduate Program in Science and Biotechnology, Biology Institute, Fluminense Federal University (UFF), Niterói-RJ, 24020-141, Brazil.
- Microbial Technology Laboratory, Pharmaceutical Technology Department, Faculty of Pharmacy, Fluminense Federal University (UFF), Niterói-RJ, 24241-000, Brazil.
- Ecology of Microbial Process Laboratory, Biochemical Engineering Department, Chemical School, Technology Center, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro-RJ, 21941-909, Brazil.
| | - Simone Santos de Sousa Oliveira
- Graduate Program in Science and Biotechnology, Biology Institute, Fluminense Federal University (UFF), Niterói-RJ, 24020-141, Brazil
- Microbial Technology Laboratory, Pharmaceutical Technology Department, Faculty of Pharmacy, Fluminense Federal University (UFF), Niterói-RJ, 24241-000, Brazil
| | - Sara Fernandes Lima
- Microbial Technology Laboratory, Pharmaceutical Technology Department, Faculty of Pharmacy, Fluminense Federal University (UFF), Niterói-RJ, 24241-000, Brazil
| | - Rodrigo Pires do Nascimento
- Ecology of Microbial Process Laboratory, Biochemical Engineering Department, Chemical School, Technology Center, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro-RJ, 21941-909, Brazil
| | - Andrea Regina de Souza Baptista
- Center for Microorganisms Investigation, Microbiology and Parasitology Department, Biomedical Institute, Fluminense Federal University (UFF), Niterói-RJ, 24020-141, Brazil
| | - Sorele Batista Fiaux
- Microbial Technology Laboratory, Pharmaceutical Technology Department, Faculty of Pharmacy, Fluminense Federal University (UFF), Niterói-RJ, 24241-000, Brazil
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30
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Rafieenia R, Atkinson E, Ledesma-Amaro R. Division of labor for substrate utilization in natural and synthetic microbial communities. Curr Opin Biotechnol 2022; 75:102706. [DOI: 10.1016/j.copbio.2022.102706] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/07/2022] [Accepted: 02/15/2022] [Indexed: 01/30/2023]
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31
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Vaiana CA, Kim H, Cottet J, Oai K, Ge Z, Conforti K, King AM, Meyer AJ, Chen H, Voigt CA, Buie CR. Characterizing chemical signaling between engineered "microbial sentinels" in porous microplates. Mol Syst Biol 2022; 18:e10785. [PMID: 35315586 PMCID: PMC8938921 DOI: 10.15252/msb.202110785] [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: 11/01/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 11/11/2022] Open
Abstract
Living materials combine a material scaffold, that is often porous, with engineered cells that perform sensing, computing, and biosynthetic tasks. Designing such systems is difficult because little is known regarding signaling transport parameters in the material. Here, the development of a porous microplate is presented. Hydrogel barriers between wells have a porosity of 60% and a tortuosity factor of 1.6, allowing molecular diffusion between wells. The permeability of dyes, antibiotics, inducers, and quorum signals between wells were characterized. A “sentinel” strain was constructed by introducing orthogonal sensors into the genome of Escherichia coli MG1655 for IPTG, anhydrotetracycline, L‐arabinose, and four quorum signals. The strain’s response to inducer diffusion through the wells was quantified up to 14 mm, and quorum and antibacterial signaling were measured over 16 h. Signaling distance is dictated by hydrogel adsorption, quantified using a linear finite element model that yields adsorption coefficients from 0 to 0.1 mol m−3. Parameters derived herein will aid the design of living materials for pathogen remediation, computation, and self‐organizing biofilms.
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Affiliation(s)
- Christopher A Vaiana
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hyungseok Kim
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Cottet
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Keiko Oai
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhifei Ge
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kameron Conforti
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew M King
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adam J Meyer
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haorong Chen
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cullen R Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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32
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Smith JM, Chowdhry R, Booth MJ. Controlling Synthetic Cell-Cell Communication. Front Mol Biosci 2022; 8:809945. [PMID: 35071327 PMCID: PMC8766733 DOI: 10.3389/fmolb.2021.809945] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/13/2021] [Indexed: 11/28/2022] Open
Abstract
Synthetic cells, which mimic cellular function within a minimal compartment, are finding wide application, for instance in studying cellular communication and as delivery devices to living cells. However, to fully realise the potential of synthetic cells, control of their function is vital. An array of tools has already been developed to control the communication of synthetic cells to neighbouring synthetic cells or living cells. These tools use either chemical inputs, such as small molecules, or physical inputs, such as light. Here, we examine these current methods of controlling synthetic cell communication and consider alternative mechanisms for future use.
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Affiliation(s)
| | | | - Michael J. Booth
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
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33
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Parsed synthesis of pyocyanin via co-culture enables context-dependent intercellular redox communication. Microb Cell Fact 2021; 20:215. [PMID: 34819093 PMCID: PMC8611841 DOI: 10.1186/s12934-021-01703-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/06/2021] [Indexed: 12/04/2022] Open
Abstract
Background Microbial co-cultures and consortia are of interest in cell-based molecular production and even as “smart” therapeutics in that one can take advantage of division of labor and specialization to expand both the range of available functions and mechanisms for control. The development of tools that enable coordination and modulation of consortia will be crucial for future application of multi-population cultures. In particular, these systems would benefit from an expanded toolset that enables orthogonal inter-strain communication. Results We created a co-culture for the synthesis of a redox-active phenazine signaling molecule, pyocyanin (PYO), by dividing its synthesis into the generation of its intermediate, phenazine carboxylic acid (PCA) from the first strain, followed by consumption of PCA and generation of PYO in a second strain. Interestingly, both PCA and PYO can be used to actuate gene expression in cells engineered with the soxRS oxidative stress regulon, although importantly this signaling activity was found to depend on growth media. That is, like other signaling motifs in bacterial systems, the signaling activity is context dependent. We then used this co-culture’s phenazine signals in a tri-culture to modulate gene expression and production of three model products: quorum sensing molecule autoinducer-1 and two fluorescent marker proteins, eGFP and DsRed. We also showed how these redox-based signals could be intermingled with other quorum-sensing (QS) signals which are more commonly used in synthetic biology, to control complex behaviors. To provide control over product synthesis in the tri-cultures, we also showed how a QS-induced growth control module could guide metabolic flux in one population and at the same time guide overall tri-culture function. Specifically, we showed that phenazine signal recognition, enabled through the oxidative stress response regulon soxRS, was dependent on media composition such that signal propagation within our parsed synthetic system could guide different desired outcomes based on the prevailing environment. In doing so, we expanded the range of signaling molecules available for coordination and the modes by which they can be utilized to influence overall function of a multi-population culture. Conclusions Our results show that redox-based signaling can be intermingled with other quorum sensing signaling in ways that enable user-defined control of microbial consortia yielding various outcomes defined by culture medium. Further, we demonstrated the utility of our previously designed growth control module in influencing signal propagation and metabolic activity is unimpeded by orthogonal redox-based signaling. By exploring novel multi-modal strategies for guiding communication and consortia outcome, the concepts introduced here may prove to be useful for coordination of multiple populations within complex microbial systems. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01703-2.
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A light tunable differentiation system for the creation and control of consortia in yeast. Nat Commun 2021; 12:5829. [PMID: 34611168 PMCID: PMC8492667 DOI: 10.1038/s41467-021-26129-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
Artificial microbial consortia seek to leverage division-of-labour to optimize function and possess immense potential for bioproduction. Co-culturing approaches, the preferred mode of generating a consortium, remain limited in their ability to give rise to stable consortia having finely tuned compositions. Here, we present an artificial differentiation system in budding yeast capable of generating stable microbial consortia with custom functionalities from a single strain at user-defined composition in space and in time based on optogenetically-driven genetic rewiring. Owing to fast, reproducible, and light-tunable dynamics, our system enables dynamic control of consortia composition in continuous cultures for extended periods. We further demonstrate that our system can be extended in a straightforward manner to give rise to consortia with multiple subpopulations. Our artificial differentiation strategy establishes a novel paradigm for the creation of complex microbial consortia that are simple to implement, precisely controllable, and versatile to use.
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35
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Espinosa-Ortiz EJ, Rene ER, Gerlach R. Potential use of fungal-bacterial co-cultures for the removal of organic pollutants. Crit Rev Biotechnol 2021; 42:361-383. [PMID: 34325585 DOI: 10.1080/07388551.2021.1940831] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fungi and bacteria coexist in a wide variety of natural and artificial environments which can lead to their association and interaction - ranging from antagonism to cooperation - that can affect the survival, colonization, spatial distribution and stress resistance of the interacting partners. The use of polymicrobial cultivation approaches has facilitated a more thorough understanding of microbial dynamics in mixed microbial communities, such as those composed of fungi and bacteria, and their influence on ecosystem functions. Mixed (multi-domain) microbial communities exhibit unique associations and interactions that could result in more efficient systems for the degradation and removal of organic pollutants. Several previous studies have reported enhanced biodegradation of certain pollutants when using combined fungal-bacterial treatments compared to pure cultures or communities of either fungi or bacteria (single domain systems). This article reviews: (i) the mechanisms of pollutant degradation that can occur in fungal-bacterial systems (e.g.: co-degradation, production of secondary metabolites, enhancement of degradative enzyme production, and transport of bacteria by fungal mycelia); (ii) case studies using fungal-bacterial co-cultures for the removal of various organic pollutants (synthetic dyes, polycyclic aromatic hydrocarbons, pesticides, and other trace or volatile organic compounds) in different environmental matrices (e.g. water, gas/vapors, soil); (iii) the key aspects of engineering artificial fungal-bacterial co-cultures, and (iv) the current challenges and future perspectives of using fungal-bacterial co-cultures for environmental remediation.
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Affiliation(s)
- Erika J Espinosa-Ortiz
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Eldon R Rene
- Department of Water Supply, Sanitary and Environmental Engineering, IHE Delft Institute for Water Education, 2601DA Delft, The Netherlands
| | - Robin Gerlach
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
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Liu X, Wang W, Li J, Li Y, Zhang J, Tan H. A widespread response of Gram-negative bacterial acyl-homoserine lactone receptors to Gram-positive Streptomyces γ-butyrolactone signaling molecules. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1575-1589. [PMID: 34319534 DOI: 10.1007/s11427-021-1956-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 05/25/2021] [Indexed: 11/26/2022]
Abstract
Cell-cell communication is critical for bacterial survival in natural habitats, in which miscellaneous regulatory networks are encompassed. However, elucidating the interaction networks of a microbial community has been hindered by the population complexity. This study reveals that γ-butyrolactone (GBL) molecules from Streptomyces species, the major antibiotic producers, can directly bind to the acyl-homoserine lactone (AHL) receptor of Chromobacterium violaceum and influence violacein production controlled by the quorum sensing (QS) system. Subsequently, the widespread responses of more Gram-negative bacterial AHL receptors to Gram-positive Streptomyces signaling molecules are unveiled. Based on the cross-talk between GBL and AHL signaling systems, combinatorial regulatory circuits (CRC) are designed and proved to be workable in Escherichia coli (E. coli). It is significant that the QS systems of Gram-positive and Gram-negative bacteria can be bridged via native Streptomyces signaling molecules. These findings pave a new path for unlocking the comprehensive cell-cell communications in microbial communities and facilitate the exploitation of innovative regulatory elements for synthetic biology.
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Affiliation(s)
- Xiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenxi Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junyue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Wu S, Xue Y, Yang S, Xu C, Liu C, Liu X, Liu J, Zhu H, Zhao GR, Yang A, Qiao J. Combinational quorum sensing devices for dynamic control in cross-feeding cocultivation. Metab Eng 2021; 67:186-197. [PMID: 34229080 DOI: 10.1016/j.ymben.2021.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/26/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Quorum sensing (QS) offers cell density dependent dynamic regulations in cell culture through devices such as synchronized lysis circuit (SLC) and metabolic toggle switch (MTS). However, there is still a lack of studies on cocultivation with a combination of different QS-based devices. Taking the production of isopropanol and salidroside as case studies, we have mathematically modeled a comprehensive set of QS-regulated cocultivation schemes and constructed experimental combinations of QS devices, respectively, to evaluate their feasibility and optimality for regulating growth competition and corporative production. Glucose split ratio is proposed for the analysis of competition between cell growth and targeted production. Results show that the combination of different QS devices across multiple members offers a new tool with the potential to effectively coordinate synthetic microbial consortia for achieving high product titer in cross-feeding cocultivation. It is also evident that the performance of such systems is significantly affected by dynamic characteristics of chosen QS devices, carbon source control and the operational settings. This study offers insights for future applications of combinational QS devices in synthetic microbial consortia.
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Affiliation(s)
- Shengbo Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, China
| | - Yanting Xue
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Shujuan Yang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Chengyang Xu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Chunjiang Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
| | - Xue Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Jiaheng Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Hongji Zhu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Guang-Rong Zhao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Aidong Yang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK.
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China.
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Castle SD, Grierson CS, Gorochowski TE. Towards an engineering theory of evolution. Nat Commun 2021; 12:3326. [PMID: 34099656 PMCID: PMC8185075 DOI: 10.1038/s41467-021-23573-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
Biological technologies are fundamentally unlike any other because biology evolves. Bioengineering therefore requires novel design methodologies with evolution at their core. Knowledge about evolution is currently applied to the design of biosystems ad hoc. Unless we have an engineering theory of evolution, we will neither be able to meet evolution's potential as an engineering tool, nor understand or limit its unintended consequences for our biological designs. Here, we propose the evotype as a helpful concept for engineering the evolutionary potential of biosystems, or other self-adaptive technologies, potentially beyond the realm of biology.
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Affiliation(s)
- Simeon D Castle
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Claire S Grierson
- School of Biological Sciences, University of Bristol, Bristol, UK
- BrisSynBio, University of Bristol, Bristol, UK
| | - Thomas E Gorochowski
- School of Biological Sciences, University of Bristol, Bristol, UK.
- BrisSynBio, University of Bristol, Bristol, UK.
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39
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Kelly EE, Fischer AM, Collins CH. Drawing up a collaborative contract: Amino acid cross-feeding between interspecies bacterial pairs. Biotechnol Bioeng 2021; 118:3138-3149. [PMID: 34027999 DOI: 10.1002/bit.27837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/09/2021] [Accepted: 05/05/2021] [Indexed: 01/04/2023]
Abstract
Synthetic microbial communities have the potential to enable new platforms for bioproduction of biofuels and biopharmaceuticals. However, using engineered communities is often assumed to be difficult because of anticipated challenges in establishing and controlling community composition. Cross-feeding between microbial auxotrophs has the potential to facilitate coculture growth and stability through a mutualistic ecological interaction. We assessed cross-feeding between 13 Escherichia coli amino acid auxotrophs paired with a leucine auxotroph of Bacillus megaterium. We developed a minimal medium capable of supporting the growth of both bacteria and used the media to study coculture growth of the 13 interspecies pairs of auxotrophs in batch and continuous culture, as well as on semi-solid media. In batch culture, 8 of 13 pairs of auxotrophs were observed to grow in coculture. We developed a new metric to quantify the impact of cross-feeding on coculture growth. Six pairs also showed long-term stability in continuous culture, where coculture growth at different dilution rates highlighted differences in cross-feeding amongst the pairs. Finally, we found that cross-feeding-dependent growth on semi-solid media is highly stringent and enables identification of the most efficient pairs. These results demonstrate that cross-feeding is a viable approach for controlling community composition within diverse synthetic communities.
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Affiliation(s)
- Erin E Kelly
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Alexandria M Fischer
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA.,Department of Biology, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Cynthia H Collins
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA.,Department of Biology, Rensselaer Polytechnic Institute, Troy, New York, USA
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40
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Perrino G, Hadjimitsis A, Ledesma-Amaro R, Stan GB. Control engineering and synthetic biology: working in synergy for the analysis and control of microbial systems. Curr Opin Microbiol 2021; 62:68-75. [PMID: 34062481 DOI: 10.1016/j.mib.2021.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 01/12/2023]
Abstract
The implementation of novel functionalities in living cells is a key aspect of synthetic biology. In the last decade, the field of synthetic biology has made progress working in synergy with control engineering, whose solid framework has provided concepts and tools to analyse biological systems and guide their design. In this review, we briefly highlight recent work focused on the application of control theoretical concepts and tools for the analysis and design of synthetic biology systems in microbial cells.
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Affiliation(s)
- Giansimone Perrino
- Department of Bioengineering & Imperial College Centre for Synthetic Biology, Imperial College London, UK
| | - Andreas Hadjimitsis
- Department of Bioengineering & Imperial College Centre for Synthetic Biology, Imperial College London, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering & Imperial College Centre for Synthetic Biology, Imperial College London, UK
| | - Guy-Bart Stan
- Department of Bioengineering & Imperial College Centre for Synthetic Biology, Imperial College London, UK.
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41
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Wu S, Xu C, Liu J, Liu C, Qiao J. Vertical and horizontal quorum-sensing-based multicellular communications. Trends Microbiol 2021; 29:1130-1142. [PMID: 34020859 DOI: 10.1016/j.tim.2021.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022]
Abstract
Quorum sensing (QS) plays an important role in both natural and synthetic microbial systems. The complexity of QS entails multilayer controls, biomolecular crosstalk, and population-based interactions. In this review, we divide complex QS-based interactions into vertical and horizontal interactions. With respect to the former, we discuss QS-based interactions among phages, bacteria, and hosts in natural microbial systems, which are based on various QS signals and hormones. With regard to the latter, we highlight manipulations of QS-based interactions for multicomponent synthetic microbial consortia. We further present the recent and emerging applications of manipulating these interactions (collectively referred to as 'QS communication networks') in natural and synthetic microbiota. Finally, we identify key challenges in engineering diverse QS communication networks for various future applications.
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Affiliation(s)
- Shengbo Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
| | - Chengyang Xu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China
| | - Jiaheng Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China
| | - Chunjiang Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China.
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China.
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42
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Ortiz Y, Carrión J, Lahoz-Beltrá R, Gutiérrez M. A Framework for Implementing Metaheuristic Algorithms Using Intercellular Communication. Front Bioeng Biotechnol 2021; 9:660148. [PMID: 34041231 PMCID: PMC8141851 DOI: 10.3389/fbioe.2021.660148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Metaheuristics (MH) are Artificial Intelligence procedures that frequently rely on evolution. MH approximate difficult problem solutions, but are computationally costly as they explore large solution spaces. This work pursues to lay the foundations of general mappings for implementing MH using Synthetic Biology constructs in cell colonies. Two advantages of this approach are: harnessing large scale parallelism capability of cell colonies and, using existing cell processes to implement basic dynamics defined in computational versions. We propose a framework that maps MH elements to synthetic circuits in growing cell colonies to replicate MH behavior in cell colonies. Cell-cell communication mechanisms such as quorum sensing (QS), bacterial conjugation, and environmental signals map to evolution operators in MH techniques to adapt to growing colonies. As a proof-of-concept, we implemented the workflow associated to the framework: automated MH simulation generators for the gro simulator and two classes of algorithms (Simple Genetic Algorithms and Simulated Annealing) encoded as synthetic circuits. Implementation tests show that synthetic counterparts mimicking MH are automatically produced, but also that cell colony parallelism speeds up the execution in terms of generations. Furthermore, we show an example of how our framework is extended by implementing a different computational model: The Cellular Automaton.
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Affiliation(s)
- Yerko Ortiz
- School of Informatics and Telecommunications, Faculty of Engineering and Sciences, Diego Portales University, Santiago, Chile
| | - Javier Carrión
- School of Informatics and Telecommunications, Faculty of Engineering and Sciences, Diego Portales University, Santiago, Chile
| | - Rafael Lahoz-Beltrá
- Department of Biodiversity, Ecology and Evolution (Biomathematics), Faculty of Biological Sciences, Complutense University of Madrid, Madrid, Spain
| | - Martín Gutiérrez
- School of Informatics and Telecommunications, Faculty of Engineering and Sciences, Diego Portales University, Santiago, Chile
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43
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Wu Y, Wang CW, Wang D, Wei N. A Whole-Cell Biosensor for Point-of-Care Detection of Waterborne Bacterial Pathogens. ACS Synth Biol 2021; 10:333-344. [PMID: 33496568 DOI: 10.1021/acssynbio.0c00491] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water contamination by pathogenic bacteria is a major public health concern globally. Monitoring bacterial contamination in water is critically important to protect human health, but this remains a critical challenge. Engineered whole-cell biosensors created through synthetic biology hold great promise for rapid and cost-effective detection of waterborne pathogens. In this study, we created a novel whole-cell biosensor to detect water contamination by Pseudomonas aeruginosa and Burkholderia pseudomallei, which are two critical bacterial pathogens and are recognized as common causative agents for waterborne diseases. The biosensor detects the target bacterial pathogens by responding to the relevant quorum sensing signal molecules. Particularly, this study constructed and characterized the biosensor on the basis of the QscR quorum sensing signal system for the first time. We first designed and constructed a QscR on the basis of the sensing module in the E. coli host cell and integrated the QscR sensing module with a reporting module that expressed an enhanced green fluorescent protein (EGFP). The results demonstrated that the biosensor had high sensitivity in response to the quorum sensing signals of the target bacterial pathogens. We further engineered a biosensor that expressed a red pigment lycopene in the reporting module to produce a visible signal readout for the pathogen detection. Additionally, we investigated the feasibility of a paper-based assay by immobilizing the lycopene-based whole-cell biosensor on paper with the aim to build a prototype for developing portable detection devices. The biosensor would provide a simple and inexpensive alternative for timely and point-of-care detection of water contamination and protect human health.
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44
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Karkaria BD, Fedorec AJH, Barnes CP. Automated design of synthetic microbial communities. Nat Commun 2021; 12:672. [PMID: 33510148 PMCID: PMC7844305 DOI: 10.1038/s41467-020-20756-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022] Open
Abstract
Microbial species rarely exist in isolation. In naturally occurring microbial systems there is strong evidence for a positive relationship between species diversity and productivity of communities. The pervasiveness of these communities in nature highlights possible advantages for genetically engineered strains to exist in cocultures as well. Building synthetic microbial communities allows us to create distributed systems that mitigate issues often found in engineering a monoculture, especially as functional complexity increases. Here, we demonstrate a methodology for designing robust synthetic communities that include competition for nutrients, and use quorum sensing to control amensal bacteriocin interactions in a chemostat environment. We computationally explore all two- and three- strain systems, using Bayesian methods to perform model selection, and identify the most robust candidates for producing stable steady state communities. Our findings highlight important interaction motifs that provide stability, and identify requirements for selecting genetic parts and further tuning the community composition.
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Affiliation(s)
- Behzad D Karkaria
- Department of Cell & Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Alex J H Fedorec
- Department of Cell & Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Chris P Barnes
- Department of Cell & Developmental Biology, University College London, London, WC1E 6BT, UK.
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
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45
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Krieger AG, Zhang J, Lin XN. Temperature regulation as a tool to program synthetic microbial community composition. Biotechnol Bioeng 2021; 118:1381-1392. [PMID: 33399224 DOI: 10.1002/bit.27662] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 11/07/2022]
Abstract
Engineering of synthetic microbial communities is emerging as a powerful new paradigm for performing various industrially, medically, and environmentally important processes. To reach the fullest potential, however, this approach requires further development in many aspects, a key one being regulating the community composition. Here we leverage well-established mechanisms in ecology which govern the relative abundance of multispecies ecosystems and develop a new tool for programming the composition of synthetic microbial communities. Using a simple model system consisting of two microorganisms Escherichia coli and Pseudomonas putida, which occupy different but partially overlapping thermal niches, we demonstrated that temperature regulation could be used to enable coexistence and program the community composition. We first investigated a constant temperature regime and showed that different temperatures led to different community compositions. Next, we invented a new cycling temperature regime and showed that it can dynamically tune the microbial community, achieving a wide range of compositions depending on parameters that are readily manipulatable. Our work provides conclusive proof of concept that temperature regulation is a versatile and powerful tool capable of programming compositions of synthetic microbial communities.
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Affiliation(s)
- Adam G Krieger
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Jiahao Zhang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Xiaoxia N Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
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46
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Tas H, Grozinger L, Stoof R, de Lorenzo V, Goñi-Moreno Á. Contextual dependencies expand the re-usability of genetic inverters. Nat Commun 2021; 12:355. [PMID: 33441561 PMCID: PMC7806840 DOI: 10.1038/s41467-020-20656-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 12/02/2020] [Indexed: 01/29/2023] Open
Abstract
The implementation of Boolean logic circuits in cells have become a very active field within synthetic biology. Although these are mostly focussed on the genetic components alone, the context in which the circuit performs is crucial for its outcome. We characterise 20 genetic NOT logic gates in up to 7 bacterial-based contexts each, to generate 135 different functions. The contexts we focus on are combinations of four plasmid backbones and three hosts, two Escherichia coli and one Pseudomonas putida strains. Each gate shows seven different dynamic behaviours, depending on the context. That is, gates can be fine-tuned by changing only contextual parameters, thus improving the compatibility between gates. Finally, we analyse portability by measuring, scoring, and comparing gate performance across contexts. Rather than being a limitation, we argue that the effect of the genetic background on synthetic constructs expands functionality, and advocate for considering context as a fundamental design parameter.
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Affiliation(s)
- Huseyin Tas
- grid.428469.50000 0004 1794 1018Systems Biology Department, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, 28049 Spain
| | - Lewis Grozinger
- grid.1006.70000 0001 0462 7212School of Computing, Newcastle University, Newcastle Upon Tyne, NE4 5TG UK
| | - Ruud Stoof
- grid.1006.70000 0001 0462 7212School of Computing, Newcastle University, Newcastle Upon Tyne, NE4 5TG UK
| | - Victor de Lorenzo
- grid.428469.50000 0004 1794 1018Systems Biology Department, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, 28049 Spain
| | - Ángel Goñi-Moreno
- grid.1006.70000 0001 0462 7212School of Computing, Newcastle University, Newcastle Upon Tyne, NE4 5TG UK ,grid.419190.40000 0001 2300 669XCentro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politénica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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Autonomous and Assisted Control for Synthetic Microbiology. Int J Mol Sci 2020; 21:ijms21239223. [PMID: 33287299 PMCID: PMC7731081 DOI: 10.3390/ijms21239223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/17/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Abstract
The control of microbes and microbial consortia to achieve specific functions requires synthetic circuits that can reliably cope with internal and external perturbations. Circuits that naturally evolved to regulate biological functions are frequently robust to alterations in their parameters. As the complexity of synthetic circuits increases, synthetic biologists need to implement such robust control "by design". This is especially true for intercellular signaling circuits for synthetic consortia, where robustness is highly desirable, but its mechanisms remain unclear. Cybergenetics, the interface between synthetic biology and control theory, offers two approaches to this challenge: external (computer-aided) and internal (autonomous) control. Here, we review natural and synthetic microbial systems with robustness, and outline experimental approaches to implement such robust control in microbial consortia through population-level cybergenetics. We propose that harnessing natural intercellular circuit topologies with robust evolved functions can help to achieve similar robust control in synthetic intercellular circuits. A "hybrid biology" approach, where robust synthetic microbes interact with natural consortia and-additionally-with external computers, could become a useful tool for health and environmental applications.
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Partners for life: building microbial consortia for the future. Curr Opin Biotechnol 2020; 66:292-300. [PMID: 33202280 DOI: 10.1016/j.copbio.2020.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/14/2020] [Accepted: 10/05/2020] [Indexed: 01/02/2023]
Abstract
New technologies have allowed researchers to better design, build, and analyze complex consortia. These developments are fueling a wider implementation of consortium-based bioprocessing by leveraging synthetic biology, delivering on the field's multitudinous promises of higher efficiencies, superior resiliency, augmented capabilities, and modular bioprocessing. Here we chronicle current progress by presenting a range of screening, computational, and biomolecular tools enabling robust population control, efficient division of labor, and programmatic spatial organization; furthermore, we detail corresponding advancements in areas including machine learning, biocontainment, and standardization. Additionally, we show applications in myriad sectors, including medicine, energy and waste sustainability, chemical production, agriculture, and biosensors. Concluding remarks outline areas of growth that will promote the utilization of complex community structures across the biotechnology spectrum.
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Jiang W, He X, Luo Y, Mu Y, Gu F, Liang Q, Qi Q. Two Completely Orthogonal Quorum Sensing Systems with Self-Produced Autoinducers Enable Automatic Delayed Cascade Control. ACS Synth Biol 2020; 9:2588-2599. [PMID: 32786361 DOI: 10.1021/acssynbio.0c00370] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The existence of crosstalk between quorum sensing systems limits their application in a complex environment. In this study, two completely orthogonal quorum sensing systems with self-produced autoinducers were built in one cell to enable the systems to be signal orthogonal and promoter orthogonal to each other. The systems were designed on the basis of the las system from Pseudomonas aeruginosa and the tra system from Agrobacterium tumefaciens. Both were optimized with respect to the orthogonality of signals and promoters by using a series of synthetic biology strategies and high-throughput screening. The systems were applied intracellularly, and an automatic delayed cascade circuit was successfully demonstrated, which can realize sequential gene expression without exogenous inducer. This circuit provides a new tool for biotechnological applications, such as metabolic regulation, that require sequential gene control. This cascade model expands the toolkit of synthetic biology research and indicates a high application potential of quorum sensing systems that are orthogonal to each other.
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Affiliation(s)
- Wei Jiang
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Xinyuan He
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Yue Luo
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Yunlan Mu
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Fei Gu
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
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Brown B, Bartley B, Beal J, Bird JE, Goñi-Moreno Á, McLaughlin JA, Mısırlı G, Roehner N, Skelton DJ, Poh CL, Ofiteru ID, James K, Wipat A. Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL). ACS Synth Biol 2020; 9:2410-2417. [PMID: 32786354 DOI: 10.1021/acssynbio.0c00176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Synthetic biology aims to develop novel biological systems and increase their reproducibility using engineering principles such as standardization and modularization. It is important that these systems can be represented and shared in a standard way to ensure they can be easily understood, reproduced, and utilized by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterization. Previously, this standard has only been used to represent designs in systems where the same design is implemented in every cell; however, there is also much interest in multicellular systems, in which designs involve a mixture of different types of cells with differing genotype and phenotype. Here, we show how the SBOL standard can be used to represent multicellular systems, and, hence, how researchers can better share designs with the community and reliably document intended system functionality.
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Affiliation(s)
- Bradley Brown
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Bryan Bartley
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Jasmine E. Bird
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Ángel Goñi-Moreno
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, United Kingdom
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politénica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Campus de Montegancedo-UPM, 28223 Pozuelo de Alarcon, Madrid, Spain
| | | | - Göksel Mısırlı
- School of Computing and Mathematics, Keele University, Newcastle ST5 5BG, United Kingdom
| | - Nicholas Roehner
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - David James Skelton
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, United Kingdom
| | - Chueh Loo Poh
- Department of Biomedical Engineering and NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore
| | - Irina Dana Ofiteru
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Katherine James
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, United Kingdom
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