1
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Chaisupa P, Wright RC. State-of-the-art in engineering small molecule biosensors and their applications in metabolic engineering. SLAS Technol 2024; 29:100113. [PMID: 37918525 PMCID: PMC11314541 DOI: 10.1016/j.slast.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
Genetically encoded biosensors are crucial for enhancing our understanding of how molecules regulate biological systems. Small molecule biosensors, in particular, help us understand the interaction between chemicals and biological processes. They also accelerate metabolic engineering by increasing screening throughput and eliminating the need for sample preparation through traditional chemical analysis. Additionally, they offer significantly higher spatial and temporal resolution in cellular analyte measurements. In this review, we discuss recent progress in in vivo biosensors and control systems-biosensor-based controllers-for metabolic engineering. We also specifically explore protein-based biosensors that utilize less commonly exploited signaling mechanisms, such as protein stability and induced degradation, compared to more prevalent transcription factor and allosteric regulation mechanism. We propose that these lesser-used mechanisms will be significant for engineering eukaryotic systems and slower-growing prokaryotic systems where protein turnover may facilitate more rapid and reliable measurement and regulation of the current cellular state. Lastly, we emphasize the utilization of cutting-edge and state-of-the-art techniques in the development of protein-based biosensors, achieved through rational design, directed evolution, and collaborative approaches.
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Affiliation(s)
- Patarasuda Chaisupa
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States; Translational Plant Sciences Center (TPSC), Virginia Tech, Blacksburg, VA 24061, United States.
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2
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Goshisht MK. Machine Learning and Deep Learning in Synthetic Biology: Key Architectures, Applications, and Challenges. ACS OMEGA 2024; 9:9921-9945. [PMID: 38463314 PMCID: PMC10918679 DOI: 10.1021/acsomega.3c05913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 03/12/2024]
Abstract
Machine learning (ML), particularly deep learning (DL), has made rapid and substantial progress in synthetic biology in recent years. Biotechnological applications of biosystems, including pathways, enzymes, and whole cells, are being probed frequently with time. The intricacy and interconnectedness of biosystems make it challenging to design them with the desired properties. ML and DL have a synergy with synthetic biology. Synthetic biology can be employed to produce large data sets for training models (for instance, by utilizing DNA synthesis), and ML/DL models can be employed to inform design (for example, by generating new parts or advising unrivaled experiments to perform). This potential has recently been brought to light by research at the intersection of engineering biology and ML/DL through achievements like the design of novel biological components, best experimental design, automated analysis of microscopy data, protein structure prediction, and biomolecular implementations of ANNs (Artificial Neural Networks). I have divided this review into three sections. In the first section, I describe predictive potential and basics of ML along with myriad applications in synthetic biology, especially in engineering cells, activity of proteins, and metabolic pathways. In the second section, I describe fundamental DL architectures and their applications in synthetic biology. Finally, I describe different challenges causing hurdles in the progress of ML/DL and synthetic biology along with their solutions.
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Affiliation(s)
- Manoj Kumar Goshisht
- Department of Chemistry, Natural and
Applied Sciences, University of Wisconsin—Green
Bay, Green
Bay, Wisconsin 54311-7001, United States
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3
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Maharjan A, Park JH. Cell-free protein synthesis system: A new frontier for sustainable biotechnology-based products. Biotechnol Appl Biochem 2023; 70:2136-2149. [PMID: 37735977 DOI: 10.1002/bab.2514] [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: 05/31/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Cell-free protein synthesis (CFPS) system is an innovative technology with a wide range of potential applications that could challenge current thinking and provide solutions to environmental and health issues. CFPS system has been demonstrated to be a successful way of producing biomolecules in a variety of applications, including the biomedical industry. Although there are still obstacles to overcome, its ease of use, versatility, and capacity for integration with other technologies open the door for it to continue serving as a vital instrument in synthetic biology research and industry. In this review, we mainly focus on the cell-free based platform for various product productions. Moreover, the challenges in the bio-therapeutic aspect using cell-free systems and their future prospective for the improvement and sustainability of the cell free systems.
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Affiliation(s)
- Anoth Maharjan
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
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4
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Bezold F, Scheffer J, Wendering P, Razaghi-Moghadam Z, Trauth J, Pook B, Nußhär H, Hasenjäger S, Nikoloski Z, Essen LO, Taxis C. Optogenetic control of Cdc48 for dynamic metabolic engineering in yeast. Metab Eng 2023; 79:97-107. [PMID: 37422133 DOI: 10.1016/j.ymben.2023.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/10/2023]
Abstract
Dynamic metabolic engineering is a strategy to switch key metabolic pathways in microbial cell factories from biomass generation to accumulation of target products. Here, we demonstrate that optogenetic intervention in the cell cycle of budding yeast can be used to increase production of valuable chemicals, such as the terpenoid β-carotene or the nucleoside analog cordycepin. We achieved optogenetic cell-cycle arrest in the G2/M phase by controlling activity of the ubiquitin-proteasome system hub Cdc48. To analyze the metabolic capacities in the cell cycle arrested yeast strain, we studied their proteomes by timsTOF mass spectrometry. This revealed widespread, but highly distinct abundance changes of metabolic key enzymes. Integration of the proteomics data in protein-constrained metabolic models demonstrated modulation of fluxes directly associated with terpenoid production as well as metabolic subsystems involved in protein biosynthesis, cell wall synthesis, and cofactor biosynthesis. These results demonstrate that optogenetically triggered cell cycle intervention is an option to increase the yields of compounds synthesized in a cellular factory by reallocation of metabolic resources.
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Affiliation(s)
- Filipp Bezold
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Johannes Scheffer
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Philipp Wendering
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Zahra Razaghi-Moghadam
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Jonathan Trauth
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Bastian Pook
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Hagen Nußhär
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Sophia Hasenjäger
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany.
| | - Christof Taxis
- Department of Biology/Genetics, Philipps-University Marburg, 35032, Marburg, Germany; School of Science and Technology, University Siegen, 57076, Siegen, Germany.
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5
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Chen Y, Gin JW, Wang Y, de Raad M, Tan S, Hillson NJ, Northen TR, Adams PD, Petzold CJ. Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format. PLoS One 2023; 18:e0288102. [PMID: 37418444 DOI: 10.1371/journal.pone.0288102] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/20/2023] [Indexed: 07/09/2023] Open
Abstract
Plate-based proteomic sample preparation offers a solution to the large sample throughput demands in the biotechnology field where hundreds or thousands of engineered microbes are constructed for testing is routine. Meanwhile, sample preparation methods that work efficiently on broader microbial groups are desirable for new applications of proteomics in other fields, such as microbial communities. Here, we detail a step-by-step protocol that consists of cell lysis in an alkaline chemical buffer (NaOH/SDS) followed by protein precipitation with high-ionic strength acetone in 96-well format. The protocol works for a broad range of microbes (e.g., Gram-negative bacteria, Gram-positive bacteria, non-filamentous fungi) and the resulting proteins are ready for tryptic digestion for bottom-up quantitative proteomic analysis without the need for desalting column cleanup. The yield of protein using this protocol increases linearly with respect to the amount of starting biomass from 0.5-2.0 OD*mL of cells. By using a bench-top automated liquid dispenser, a cost-effective and environmentally-friendly option to eliminating pipette tips and reducing reagent waste, the protocol takes approximately 30 minutes to extract protein from 96 samples. Tests on mock mixtures showed expected results that the biomass composition structure is in close agreement with the experimental design. Lastly, we applied the protocol for the composition analysis of a synthetic community of environmental isolates grown on two different media. This protocol has been developed to facilitate rapid, low-variance sample preparation of hundreds of samples and allow flexibility for future protocol development.
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Affiliation(s)
- Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Jennifer W Gin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Ying Wang
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Markus de Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Stephen Tan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Nathan J Hillson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Trent R Northen
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Paul D Adams
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America
- Molecular Biophysics and Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
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6
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Demeester W, De Baets J, Duchi D, De Mey M, De Paepe B. MoBioS: Modular Platform Technology for High-Throughput Construction and Characterization of Tunable Transcriptional Biological Sensors. BIOSENSORS 2023; 13:590. [PMID: 37366955 DOI: 10.3390/bios13060590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/16/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
All living organisms have evolved and fine-tuned specialized mechanisms to precisely monitor a vast array of different types of molecules. These natural mechanisms can be sourced by researchers to build Biological Sensors (BioS) by combining them with an easily measurable output, such as fluorescence. Because they are genetically encoded, BioS are cheap, fast, sustainable, portable, self-generating and highly sensitive and specific. Therefore, BioS hold the potential to become key enabling tools that stimulate innovation and scientific exploration in various disciplines. However, the main bottleneck in unlocking the full potential of BioS is the fact that there is no standardized, efficient and tunable platform available for the high-throughput construction and characterization of biosensors. Therefore, a modular, Golden Gate-based construction platform, called MoBioS, is introduced in this article. It allows for the fast and easy creation of transcription factor-based biosensor plasmids. As a proof of concept, its potential is demonstrated by creating eight different, functional and standardized biosensors that detect eight diverse molecules of industrial interest. In addition, the platform contains novel built-in features to facilitate fast and efficient biosensor engineering and response curve tuning.
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Affiliation(s)
- Wouter Demeester
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
| | - Jasmine De Baets
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
| | - Dries Duchi
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
| | - Brecht De Paepe
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
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7
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Gurdo N, Volke DC, McCloskey D, Nikel PI. Automating the design-build-test-learn cycle towards next-generation bacterial cell factories. N Biotechnol 2023; 74:1-15. [PMID: 36736693 DOI: 10.1016/j.nbt.2023.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/15/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023]
Abstract
Automation is playing an increasingly significant role in synthetic biology. Groundbreaking technologies, developed over the past 20 years, have enormously accelerated the construction of efficient microbial cell factories. Integrating state-of-the-art tools (e.g. for genome engineering and analytical techniques) into the design-build-test-learn cycle (DBTLc) will shift the metabolic engineering paradigm from an almost artisanal labor towards a fully automated workflow. Here, we provide a perspective on how a fully automated DBTLc could be harnessed to construct the next-generation bacterial cell factories in a fast, high-throughput fashion. Innovative toolsets and approaches that pushed the boundaries in each segment of the cycle are reviewed to this end. We also present the most recent efforts on automation of the DBTLc, which heralds a fully autonomous pipeline for synthetic biology in the near future.
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Affiliation(s)
- Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
| | - Douglas McCloskey
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark.
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8
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Park H, Faulkner M, Toogood HS, Chen GQ, Scrutton N. Online Omics Platform Expedites Industrial Application of Halomonas bluephagenesis TD1.0. Bioinform Biol Insights 2023; 17:11779322231171779. [PMID: 37200674 PMCID: PMC10185862 DOI: 10.1177/11779322231171779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/07/2023] [Indexed: 05/20/2023] Open
Abstract
Multi-omic data mining has the potential to revolutionize synthetic biology especially in non-model organisms that have not been extensively studied. However, tangible engineering direction from computational analysis remains elusive due to the interpretability of large datasets and the difficulty in analysis for non-experts. New omics data are generated faster than our ability to use and analyse results effectively, resulting in strain development that proceeds through classic methods of trial-and-error without insight into complex cell dynamics. Here we introduce a user-friendly, interactive website hosting multi-omics data. Importantly, this new platform allows non-experts to explore questions in an industrially important chassis whose cellular dynamics are still largely unknown. The web platform contains a complete KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis derived from principal components analysis, an interactive bio-cluster heatmap analysis of genes, and the Halomonas TD1.0 genome-scale metabolic (GEM) model. As a case study of the effectiveness of this platform, we applied unsupervised machine learning to determine key differences between Halomonas bluephagenesis TD1.0 cultivated under varied conditions. Specifically, cell motility and flagella apparatus are identified to drive energy expenditure usage at different osmolarities, and predictions were verified experimentally using microscopy and fluorescence labelled flagella staining. As more omics projects are completed, this landing page will facilitate exploration and targeted engineering efforts of the robust, industrial chassis H bluephagenesis for researchers without extensive bioinformatics background.
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Affiliation(s)
- Helen Park
- EPSRC/BBSRC Future Biomanufacturing Research Hub and BBSRC Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, UK
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Matthew Faulkner
- EPSRC/BBSRC Future Biomanufacturing Research Hub and BBSRC Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, UK
| | - Helen S Toogood
- EPSRC/BBSRC Future Biomanufacturing Research Hub and BBSRC Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, UK
| | - Guo-Qiang Chen
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Nigel Scrutton
- EPSRC/BBSRC Future Biomanufacturing Research Hub and BBSRC Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, UK
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9
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MYC2: A Master Switch for Plant Physiological Processes and Specialized Metabolite Synthesis. Int J Mol Sci 2023; 24:ijms24043511. [PMID: 36834921 PMCID: PMC9963318 DOI: 10.3390/ijms24043511] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/27/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
The jasmonic acid (JA) signaling pathway plays important roles in plant defenses, development, and the synthesis of specialized metabolites synthesis. Transcription factor MYC2 is a major regulator of the JA signaling pathway and is involved in the regulation of plant physiological processes and specialized metabolite synthesis. Based on our understanding of the mechanism underlying the regulation of specialized metabolite synthesis in plants by the transcription factor MYC2, the use of synthetic biology approaches to design MYC2-driven chassis cells for the synthesis of specialized metabolites with high medicinal value, such as paclitaxel, vincristine, and artemisinin, seems to be a promising strategy. In this review, the regulatory role of MYC2 in JA signal transduction of plants to biotic and abiotic stresses, plant growth, development and specialized metabolite synthesis is described in detail, which will provide valuable reference for the use of MYC2 molecular switches to regulate plant specialized metabolite biosynthesis.
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10
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Rizzo P, Chavez BG, Leite Dias S, D'Auria JC. Plant synthetic biology: from inspiration to augmentation. Curr Opin Biotechnol 2023; 79:102857. [PMID: 36502769 DOI: 10.1016/j.copbio.2022.102857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022]
Abstract
Although it is still in its infancy, synthetic biology has the capacity to face scientific and societal problems related to modern agriculture. Innovations in cloning toolkits and genetic parts allow increased precision over gene expression in planta. We review the vast spectrum of available technologies providing a practical list of toolkits that take advantage of combinatorial power to introduce/alter metabolic pathways. We highlight that rational design is inspired by deep knowledge of natural and biochemical mechanisms. Finally, we provide several examples in which modern technologies have been applied to address these critical topics. Future applications in plants include not only pathway modifications but also prospects of augmenting plant anatomical features and developmental processes.
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Affiliation(s)
- Paride Rizzo
- Metabolite Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Correnstr. 3, D-06466 Seeland, Germany
| | - Benjamin G Chavez
- Metabolite Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Correnstr. 3, D-06466 Seeland, Germany
| | - Sara Leite Dias
- Metabolite Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Correnstr. 3, D-06466 Seeland, Germany
| | - John C D'Auria
- Metabolite Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Correnstr. 3, D-06466 Seeland, Germany.
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11
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Broddrick JT, Ware MA, Jallet D, Palsson BO, Peers G. Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:603-621. [PMID: 36053127 PMCID: PMC9826171 DOI: 10.1111/tpj.15965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 06/01/2023]
Abstract
Characterizing photosynthetic productivity is necessary to understand the ecological contributions and biotechnology potential of plants, algae, and cyanobacteria. Light capture efficiency and photophysiology have long been characterized by measurements of chlorophyll fluorescence dynamics. However, these investigations typically do not consider the metabolic network downstream of light harvesting. By contrast, genome-scale metabolic models capture species-specific metabolic capabilities but have yet to incorporate the rapid regulation of the light harvesting apparatus. Here, we combine chlorophyll fluorescence parameters defining photosynthetic and non-photosynthetic yield of absorbed light energy with a metabolic model of the pennate diatom Phaeodactylum tricornutum. This integration increases the model predictive accuracy regarding growth rate, intracellular oxygen production and consumption, and metabolic pathway usage. Through the quantification of excess electron transport, we uncover the sequential activation of non-radiative energy dissipation processes, cross-compartment electron shuttling, and non-photochemical quenching as the rapid photoacclimation strategy in P. tricornutum. Interestingly, the photon absorption thresholds that trigger the transition between these mechanisms were consistent at low and high incident photon fluxes. We use this understanding to explore engineering strategies for rerouting cellular resources and excess light energy towards bioproducts in silico. Overall, we present a methodology for incorporating a common, informative data type into computational models of light-driven metabolism and show its utilization within the design-build-test-learn cycle for engineering of photosynthetic organisms.
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Affiliation(s)
- Jared T. Broddrick
- Division of Biological SciencesUniversity of California, San DiegoLa JollaCA92093USA
- Department of BioengineeringUniversity of California, San DiegoLa JollaCA92093USA
- Space Biosciences Research BranchNASA Ames Research CenterMoffett FieldCA94035USA
| | - Maxwell A. Ware
- Department of BiologyColorado State UniversityFort CollinsCO80524USA
| | - Denis Jallet
- Department of BiologyColorado State UniversityFort CollinsCO80524USA
| | - Bernhard O. Palsson
- Department of BioengineeringUniversity of California, San DiegoLa JollaCA92093USA
| | - Graham Peers
- Department of BiologyColorado State UniversityFort CollinsCO80524USA
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12
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Song Y, He S, Jopkiewicz A, Setroikromo R, van Merkerk R, Quax WJ. Development and application of CRISPR-based genetic tools in Bacillus species and Bacillus phages. J Appl Microbiol 2022; 133:2280-2298. [PMID: 35797344 PMCID: PMC9796756 DOI: 10.1111/jam.15704] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/02/2022] [Accepted: 07/06/2022] [Indexed: 01/07/2023]
Abstract
Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) system has been developed into a precise and efficient genome editing tool. Since its discovery as an adaptive immune system in prokaryotes, it has been applied in many different research fields including biotechnology and medical sciences. The high demand for rapid, highly efficient and versatile genetic tools to thrive in bacteria-based cell factories accelerates this process. This review mainly focuses on significant advancements of the CRISPR system in Bacillus subtilis, including the achievements in gene editing, and on problems still remaining. Next, we comprehensively summarize this genetic tool's up-to-date development and utilization in other Bacillus species, including B. licheniformis, B. methanolicus, B. anthracis, B. cereus, B. smithii and B. thuringiensis. Furthermore, we describe the current application of CRISPR tools in phages to increase Bacillus hosts' resistance to virulent phages and phage genetic modification. Finally, we suggest potential strategies to further improve this advanced technique and provide insights into future directions of CRISPR technologies for rendering Bacillus species cell factories more effective and more powerful.
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Affiliation(s)
- Yafeng Song
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern ChinaInstitute of Microbiology, Guangdong Acadamy of SciencesGuangzhouChina
| | - Siqi He
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Anita Jopkiewicz
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Wim J. Quax
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
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13
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Garcia BJ, Urrutia J, Zheng G, Becker D, Corbet C, Maschhoff P, Cristofaro A, Gaffney N, Vaughn M, Saxena U, Chen YP, Gordon DB, Eslami M. A toolkit for enhanced reproducibility of RNASeq analysis for synthetic biologists. SYNTHETIC BIOLOGY (OXFORD, ENGLAND) 2022; 7:ysac012. [PMID: 36035514 PMCID: PMC9408027 DOI: 10.1093/synbio/ysac012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 06/17/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022]
Abstract
Sequencing technologies, in particular RNASeq, have become critical tools in the design, build, test and learn cycle of synthetic biology. They provide a better understanding of synthetic designs, and they help identify ways to improve and select designs. While these data are beneficial to design, their collection and analysis is a complex, multistep process that has implications on both discovery and reproducibility of experiments. Additionally, tool parameters, experimental metadata, normalization of data and standardization of file formats present challenges that are computationally intensive. This calls for high-throughput pipelines expressly designed to handle the combinatorial and longitudinal nature of synthetic biology. In this paper, we present a pipeline to maximize the analytical reproducibility of RNASeq for synthetic biologists. We also explore the impact of reproducibility on the validation of machine learning models. We present the design of a pipeline that combines traditional RNASeq data processing tools with structured metadata tracking to allow for the exploration of the combinatorial design in a high-throughput and reproducible manner. We then demonstrate utility via two different experiments: a control comparison experiment and a machine learning model experiment. The first experiment compares datasets collected from identical biological controls across multiple days for two different organisms. It shows that a reproducible experimental protocol for one organism does not guarantee reproducibility in another. The second experiment quantifies the differences in experimental runs from multiple perspectives. It shows that the lack of reproducibility from these different perspectives can place an upper bound on the validation of machine learning models trained on RNASeq data.
Graphical Abstract
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Affiliation(s)
- Benjamin J Garcia
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joshua Urrutia
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA
| | | | | | | | | | - Alexander Cristofaro
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Niall Gaffney
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA
| | - Matthew Vaughn
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA
| | - Uma Saxena
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - D Benjamin Gordon
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
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14
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León-Buitimea A, Balderas-Cisneros FDJ, Garza-Cárdenas CR, Garza-Cervantes JA, Morones-Ramírez JR. Synthetic Biology Tools for Engineering Microbial Cells to Fight Superbugs. Front Bioeng Biotechnol 2022; 10:869206. [PMID: 35600895 PMCID: PMC9114757 DOI: 10.3389/fbioe.2022.869206] [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: 02/04/2022] [Accepted: 04/18/2022] [Indexed: 11/23/2022] Open
Abstract
With the increase in clinical cases of bacterial infections with multiple antibiotic resistance, the world has entered a health crisis. Overuse, inappropriate prescribing, and lack of innovation of antibiotics have contributed to the surge of microorganisms that can overcome traditional antimicrobial treatments. In 2017, the World Health Organization published a list of pathogenic bacteria, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli (ESKAPE). These bacteria can adapt to multiple antibiotics and transfer their resistance to other organisms; therefore, studies to find new therapeutic strategies are needed. One of these strategies is synthetic biology geared toward developing new antimicrobial therapies. Synthetic biology is founded on a solid and well-established theoretical framework that provides tools for conceptualizing, designing, and constructing synthetic biological systems. Recent developments in synthetic biology provide tools for engineering synthetic control systems in microbial cells. Applying protein engineering, DNA synthesis, and in silico design allows building metabolic pathways and biological circuits to control cellular behavior. Thus, synthetic biology advances have permitted the construction of communication systems between microorganisms where exogenous molecules can control specific population behaviors, induce intracellular signaling, and establish co-dependent networks of microorganisms.
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Affiliation(s)
- Angel León-Buitimea
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - Francisco de Jesús Balderas-Cisneros
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - César Rodolfo Garza-Cárdenas
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - Javier Alberto Garza-Cervantes
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - José Rubén Morones-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
- *Correspondence: José Rubén Morones-Ramírez,
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15
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Abstract
Enzymes are represented across a vast space of protein sequences and structural forms and have activities that far exceed the best chemical catalysts; however, engineering them to have novel or enhanced activity is limited by technologies for sensing product formation. Here, we describe a general and scalable approach for characterizing enzyme activity that uses the metabolism of the host cell as a biosensor by which to infer product formation. Since different products consume different molecules in their synthesis, they perturb host metabolism in unique ways that can be measured by mass spectrometry. This provides a general way by which to sense product formation, to discover unexpected products and map the effects of mutagenesis. The testing of engineered enzymes represents a bottleneck. Here the authors report a screening method combining microfluidics and mass spectrometry, to map the catalysis of a mutated enzyme, characterise the range of products generated and recover the sequences of variants with desired activities.
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16
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McNaughton AD, Bredeweg EL, Manzer J, Zucker J, Munoz Munoz N, Burnet MC, Nakayasu ES, Pomraning KR, Merkley ED, Dai Z, Chrisler WB, Baker SE, St. John PC, Kumar N. Bayesian Inference for Integrating Yarrowia lipolytica Multiomics Datasets with Metabolic Modeling. ACS Synth Biol 2021; 10:2968-2981. [PMID: 34636549 DOI: 10.1021/acssynbio.1c00267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Optimizing the metabolism of microbial cell factories for yields and titers is a critical step for economically viable production of bioproducts and biofuels. In this process, tuning the expression of individual enzymes to obtain the desired pathway flux is a challenging step, in which data from separate multiomics techniques must be integrated with existing biological knowledge to determine where changes should be made. Following a design-build-test-learn strategy, building on recent advances in Bayesian metabolic control analysis, we identify key enzymes in the oleaginous yeast Yarrowia lipolytica that correlate with the production of itaconate by integrating a metabolic model with multiomics measurements. To this extent, we quantify the uncertainty for a variety of key parameters, known as flux control coefficients (FCCs), needed to improve the bioproduction of target metabolites and statistically obtain key correlations between the measured enzymes and boundary flux. Based on the top five significant FCCs and five correlated enzymes, our results show phosphoglycerate mutase, acetyl-CoA synthetase (ACSm), carbonic anhydrase (HCO3E), pyrophosphatase (PPAm), and homoserine dehydrogenase (HSDxi) enzymes in rate-limiting reactions that can lead to increased itaconic acid production.
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Affiliation(s)
- Andrew D. McNaughton
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Erin L. Bredeweg
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - James Manzer
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jeremy Zucker
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Nathalie Munoz Munoz
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Meagan C. Burnet
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ernesto S. Nakayasu
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kyle R. Pomraning
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Eric D. Merkley
- National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ziyu Dai
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - William B. Chrisler
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Scott E. Baker
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Peter C. St. John
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Neeraj Kumar
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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17
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Mani V, Park S, Kim JA, Lee SI, Lee K. Metabolic Perturbation and Synthetic Biology Strategies for Plant Terpenoid Production-An Updated Overview. PLANTS (BASEL, SWITZERLAND) 2021; 10:2179. [PMID: 34685985 PMCID: PMC8539415 DOI: 10.3390/plants10102179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022]
Abstract
Terpenoids represent one of the high-value groups of specialized metabolites with vast structural diversity. They exhibit versatile human benefits and have been successfully exploited in several sectors of day-to-day life applications, including cosmetics, foods, and pharmaceuticals. Historically, the potential use of terpenoids is challenging, and highly hampered by their bioavailability in their natural sources. Significant progress has been made in recent years to overcome such challenges by advancing the heterologous production platforms of hosts and metabolic engineering technologies. Herein, we summarize the latest developments associated with analytical platforms, metabolic engineering, and synthetic biology, with a focus on two terpenoid classes: monoterpenoids and sesquiterpenoids. Accumulated data showed that subcellular localization of both the precursor pool and the introduced enzymes were the crucial factors for increasing the production of targeted terpenoids in plants. We believe this timely review provides a glimpse of current state-of-the-art techniques/methodologies related to terpenoid engineering that would facilitate further improvements in terpenoids research.
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Affiliation(s)
| | | | | | | | - Kijong Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (V.M.); (S.P.); (J.A.K.); (S.I.L.)
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18
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Kumashi S, Jung D, Park J, Tejedor-Sanz S, Grijalva S, Wang A, Li S, Cho HC, Ajo-Franklin C, Wang H. A CMOS Multi-Modal Electrochemical and Impedance Cellular Sensing Array for Massively Paralleled Exoelectrogen Screening. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2021; 15:221-234. [PMID: 33760741 DOI: 10.1109/tbcas.2021.3068710] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The paper presents a 256-pixel CMOS sensor array with in-pixel dual electrochemical and impedance detection modalities for rapid, multi-dimensional characterization of exoelectrogens. The CMOS IC has 16 parallel readout channels, allowing it to perform multiple measurements with a high throughput and enable the chip to handle different samples simultaneously. The chip contains a total of 2 × 256 working electrodes of size 44 μm × 52 μm, along with 16 reference electrodes of dimensions 56 μm × 399 μm and 32 counter electrodes of dimensions 399 μm × 106 μm, which together facilitate the high resolution screening of the test samples. The chip was fabricated in a standard 130nm BiCMOS process. The on-chip electrodes are subjected to additional fabrication processes, including a critical Al-etch step that ensures the excellent biocompatibility and long-term reliability of the CMOS sensor array in bio-environment. The electrochemical sensing modality is verified by detecting the electroactive analyte NaFeEDTA and the exoelectrogenic Shewanella oneidensis MR-1 bacteria, illustrating the chip's ability to quantify the generated electrochemical current and distinguish between different analyte concentrations. The impedance measurements with the HEK-293 cancer cells cultured on-chip successfully capture the cell-to-surface adhesion information between the electrodes and the cancer cells. The reported CMOS sensor array outperforms the conventional discrete setups for exoelectrogen characterization in terms of spatial resolution and speed, which demonstrates the chip's potential to radically accelerate synthetic biology engineering.
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19
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Roy S, Radivojevic T, Forrer M, Marti JM, Jonnalagadda V, Backman T, Morrell W, Plahar H, Kim J, Hillson N, Garcia Martin H. Multiomics Data Collection, Visualization, and Utilization for Guiding Metabolic Engineering. Front Bioeng Biotechnol 2021; 9:612893. [PMID: 33634086 PMCID: PMC7902046 DOI: 10.3389/fbioe.2021.612893] [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: 10/01/2020] [Accepted: 01/13/2021] [Indexed: 12/11/2022] Open
Abstract
Biology has changed radically in the past two decades, growing from a purely descriptive science into also a design science. The availability of tools that enable the precise modification of cells, as well as the ability to collect large amounts of multimodal data, open the possibility of sophisticated bioengineering to produce fuels, specialty and commodity chemicals, materials, and other renewable bioproducts. However, despite new tools and exponentially increasing data volumes, synthetic biology cannot yet fulfill its true potential due to our inability to predict the behavior of biological systems. Here, we showcase a set of computational tools that, combined, provide the ability to store, visualize, and leverage multiomics data to predict the outcome of bioengineering efforts. We show how to upload, visualize, and output multiomics data, as well as strain information, into online repositories for several isoprenol-producing strain designs. We then use these data to train machine learning algorithms that recommend new strain designs that are correctly predicted to improve isoprenol production by 23%. This demonstration is done by using synthetic data, as provided by a novel library, that can produce credible multiomics data for testing algorithms and computational tools. In short, this paper provides a step-by-step tutorial to leverage these computational tools to improve production in bioengineered strains.
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Affiliation(s)
- Somtirtha Roy
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States
| | - Tijana Radivojevic
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
| | - Mark Forrer
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States.,Sandia National Laboratories, Biomaterials and Biomanufacturing, Livermore, CA, United States
| | - Jose Manuel Marti
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
| | - Vamshi Jonnalagadda
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States
| | - Tyler Backman
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
| | - William Morrell
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States.,Sandia National Laboratories, Biomaterials and Biomanufacturing, Livermore, CA, United States
| | - Hector Plahar
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States
| | - Joonhoon Kim
- Joint BioEnergy Institute, Emeryville, CA, United States.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Nathan Hillson
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
| | - Hector Garcia Martin
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States.,Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States.,BCAM, Basque Center for Applied Mathematics, Bilbao, Spain
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20
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Kampers LFC, Koehorst JJ, van Heck RJA, Suarez-Diez M, Stams AJM, Schaap PJ. A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration. BMC Microbiol 2021; 21:9. [PMID: 33407113 PMCID: PMC7789669 DOI: 10.1186/s12866-020-02058-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Pseudomonas putida KT2440 is a metabolically versatile, HV1-certified, genetically accessible, and thus interesting microbial chassis for biotechnological applications. However, its obligate aerobic nature hampers production of oxygen sensitive products and drives up costs in large scale fermentation. The inability to perform anaerobic fermentation has been attributed to insufficient ATP production and an inability to produce pyrimidines under these conditions. Addressing these bottlenecks enabled growth under micro-oxic conditions but does not lead to growth or survival under anoxic conditions. RESULTS Here, a data-driven approach was used to develop a rational design for a P. putida KT2440 derivative strain capable of anaerobic respiration. To come to the design, data derived from a genome comparison of 1628 Pseudomonas strains was combined with genome-scale metabolic modelling simulations and a transcriptome dataset of 47 samples representing 14 environmental conditions from the facultative anaerobe Pseudomonas aeruginosa. CONCLUSIONS The results indicate that the implementation of anaerobic respiration in P. putida KT2440 would require at least 49 additional genes of known function, at least 8 genes encoding proteins of unknown function, and 3 externally added vitamins.
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Affiliation(s)
- Linde F C Kampers
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Ruben J A van Heck
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands.
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21
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Lawson CE, Martí JM, Radivojevic T, Jonnalagadda SVR, Gentz R, Hillson NJ, Peisert S, Kim J, Simmons BA, Petzold CJ, Singer SW, Mukhopadhyay A, Tanjore D, Dunn JG, Garcia Martin H. Machine learning for metabolic engineering: A review. Metab Eng 2020; 63:34-60. [PMID: 33221420 DOI: 10.1016/j.ymben.2020.10.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/22/2020] [Accepted: 10/31/2020] [Indexed: 12/14/2022]
Abstract
Machine learning provides researchers a unique opportunity to make metabolic engineering more predictable. In this review, we offer an introduction to this discipline in terms that are relatable to metabolic engineers, as well as providing in-depth illustrative examples leveraging omics data and improving production. We also include practical advice for the practitioner in terms of data management, algorithm libraries, computational resources, and important non-technical issues. A variety of applications ranging from pathway construction and optimization, to genetic editing optimization, cell factory testing, and production scale-up are discussed. Moreover, the promising relationship between machine learning and mechanistic models is thoroughly reviewed. Finally, the future perspectives and most promising directions for this combination of disciplines are examined.
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Affiliation(s)
- Christopher E Lawson
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Jose Manuel Martí
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Tijana Radivojevic
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Sai Vamshi R Jonnalagadda
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Reinhard Gentz
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nathan J Hillson
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Sean Peisert
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; University of California Davis, Davis, CA, 95616, USA
| | - Joonhoon Kim
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Pacific Northwest National Laboratory, Richland, 99354, WA, USA
| | - Blake A Simmons
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Christopher J Petzold
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Steven W Singer
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, USA
| | - Deepti Tanjore
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Advanced Biofuels and Bioproducts Process Development Unit, Emeryville, CA, 94608, USA
| | | | - Hector Garcia Martin
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Basque Center for Applied Mathematics, 48009, Bilbao, Spain; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, USA.
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22
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Streamlining the Analysis of Dynamic 13C-Labeling Patterns for the Metabolic Engineering of Corynebacterium glutamicum as l-Histidine Production Host. Metabolites 2020; 10:metabo10110458. [PMID: 33198305 PMCID: PMC7696456 DOI: 10.3390/metabo10110458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/19/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022] Open
Abstract
Today’s possibilities of genome editing easily create plentitudes of strain mutants that need to be experimentally qualified for configuring the next steps of strain engineering. The application of design-build-test-learn cycles requires the identification of distinct metabolic engineering targets as design inputs for subsequent optimization rounds. Here, we present the pool influx kinetics (PIK) approach that identifies promising metabolic engineering targets by pairwise comparison of up- and downstream 13C labeling dynamics with respect to a metabolite of interest. Showcasing the complex l-histidine production with engineered Corynebacterium glutamicuml-histidine-on-glucose yields could be improved to 8.6 ± 0.1 mol% by PIK analysis, starting from a base strain. Amplification of purA, purB, purH, and formyl recycling was identified as key targets only analyzing the signal transduction kinetics mirrored in the PIK values.
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23
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High-throughput screening for high-efficiency small-molecule biosynthesis. Metab Eng 2020; 63:102-125. [PMID: 33017684 DOI: 10.1016/j.ymben.2020.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/14/2023]
Abstract
Systems metabolic engineering faces the formidable task of rewiring microbial metabolism to cost-effectively generate high-value molecules from a variety of inexpensive feedstocks for many different applications. Because these cellular systems are still too complex to model accurately, vast collections of engineered organism variants must be systematically created and evaluated through an enormous trial-and-error process in order to identify a manufacturing-ready strain. The high-throughput screening of strains to optimize their scalable manufacturing potential requires execution of many carefully controlled, parallel, miniature fermentations, followed by high-precision analysis of the resulting complex mixtures. This review discusses strategies for the design of high-throughput, small-scale fermentation models to predict improved strain performance at large commercial scale. Established and promising approaches from industrial and academic groups are presented for both cell culture and analysis, with primary focus on microplate- and microfluidics-based screening systems.
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24
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Radivojević T, Costello Z, Workman K, Garcia Martin H. A machine learning Automated Recommendation Tool for synthetic biology. Nat Commun 2020; 11:4879. [PMID: 32978379 PMCID: PMC7519645 DOI: 10.1038/s41467-020-18008-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/27/2020] [Indexed: 01/07/2023] Open
Abstract
Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or anticancer drugs. However, traditional synthetic biology approaches involve ad-hoc engineering practices, which lead to long development times. Here, we present the Automated Recommendation Tool (ART), a tool that leverages machine learning and probabilistic modeling techniques to guide synthetic biology in a systematic fashion, without the need for a full mechanistic understanding of the biological system. Using sampling-based optimization, ART provides a set of recommended strains to be built in the next engineering cycle, alongside probabilistic predictions of their production levels. We demonstrate the capabilities of ART on simulated data sets, as well as experimental data from real metabolic engineering projects producing renewable biofuels, hoppy flavored beer without hops, fatty acids, and tryptophan. Finally, we discuss the limitations of this approach, and the practical consequences of the underlying assumptions failing.
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Affiliation(s)
- Tijana Radivojević
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Zak Costello
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kenneth Workman
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Hector Garcia Martin
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA.
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- BCAM, Basque Center for Applied Mathematics, Bilbao, 48009, Spain.
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Volk MJ, Lourentzou I, Mishra S, Vo LT, Zhai C, Zhao H. Biosystems Design by Machine Learning. ACS Synth Biol 2020; 9:1514-1533. [PMID: 32485108 DOI: 10.1021/acssynbio.0c00129] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Biosystems such as enzymes, pathways, and whole cells have been increasingly explored for biotechnological applications. However, the intricate connectivity and resulting complexity of biosystems poses a major hurdle in designing biosystems with desirable features. As -omics and other high throughput technologies have been rapidly developed, the promise of applying machine learning (ML) techniques in biosystems design has started to become a reality. ML models enable the identification of patterns within complicated biological data across multiple scales of analysis and can augment biosystems design applications by predicting new candidates for optimized performance. ML is being used at every stage of biosystems design to help find nonobvious engineering solutions with fewer design iterations. In this review, we first describe commonly used models and modeling paradigms within ML. We then discuss some applications of these models that have already shown success in biotechnological applications. Moreover, we discuss successful applications at all scales of biosystems design, including nucleic acids, genetic circuits, proteins, pathways, genomes, and bioprocesses. Finally, we discuss some limitations of these methods and potential solutions as well as prospects of the combination of ML and biosystems design.
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Lee S, Kim P. Current Status and Applications of Adaptive Laboratory Evolution in Industrial Microorganisms. J Microbiol Biotechnol 2020; 30:793-803. [PMID: 32423186 PMCID: PMC9728180 DOI: 10.4014/jmb.2003.03072] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/03/2020] [Indexed: 12/15/2022]
Abstract
Adaptive laboratory evolution (ALE) is an evolutionary engineering approach in artificial conditions that improves organisms through the imitation of natural evolution. Due to the development of multi-level omics technologies in recent decades, ALE can be performed for various purposes at the laboratory level. This review delineates the basics of the experimental design of ALE based on several ALE studies of industrial microbial strains and updates current strategies combined with progressed metabolic engineering, in silico modeling and automation to maximize the evolution efficiency. Moreover, the review sheds light on the applicability of ALE as a strain development approach that complies with non-recombinant preferences in various food industries. Overall, recent progress in the utilization of ALE for strain development leading to successful industrialization is discussed.
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Affiliation(s)
- SuRin Lee
- Department of Biotechnology, the Catholic University of Korea, Gyeonggi 14662, Republic of Korea
| | - Pil Kim
- Department of Biotechnology, the Catholic University of Korea, Gyeonggi 14662, Republic of Korea,Corresponding author Phone : +82-2164-4922 Fax : +82-2-2164-4865 E-mail:
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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28
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Katiyar P, Pandey N, Sahu KK. Biological approaches of fluoride remediation: potential for environmental clean-up. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:13044-13055. [PMID: 32146673 DOI: 10.1007/s11356-020-08224-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
Fluoride (F), anion of fluorine which is naturally present in soil and water, behaves as toxic inorganic pollutant even at lower concentration and needs immediate attention. Its interaction with flora, fauna and other forms of life, such as microbes, adversely affect various physiochemical parameters by interfering with several metabolic pathways. Conventional methods of F remediation are time-consuming, laborious and cost intensive, which renders them uneconomical for sustainable agriculture. The solution lies in cracking down this environmental contaminant by adopting economic, eco-friendly, cost-effective and modern technologies. Biological processes, viz. bioremediation involving the use of bacteria, fungi, algae and higher plants that holds promising alternative to manage F pollution, recover contaminated soil and improve vegetation. The efficiency of indigenous natural agents may be enhanced, improved and selected over the hazardous chemicals in sustainable agriculture. This review article emphasizes on various biological approaches for the remediation of F-contaminated environment, and exploring their potential applications in environmental clean-up. It further focuses on thorough systemic study of modern biotechnological approaches such as gene editing and gene manipulation techniques for enhancing the plant-microbe interactions for F degradation, drawing attention towards latest progresses in the field of microbial assisted treatment of F-contaminated ecosystems. Future research and understanding of the molecular mechanisms of F bioremediation would add on to the possibilities of the application of more competent strains showing striking results under diverse ecological conditions.
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Affiliation(s)
- Priya Katiyar
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, 492 010, India
| | - Neha Pandey
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, 492 010, India
- Kristu Jayanti College (Autonomous), K. Narayanapura, Kothanur, Bengaluru, 560 077, India
| | - Keshav Kant Sahu
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur, 492 010, India.
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Gowers GOF, Chee SM, Bell D, Suckling L, Kern M, Tew D, McClymont DW, Ellis T. Improved betulinic acid biosynthesis using synthetic yeast chromosome recombination and semi-automated rapid LC-MS screening. Nat Commun 2020; 11:868. [PMID: 32054834 PMCID: PMC7018806 DOI: 10.1038/s41467-020-14708-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/24/2020] [Indexed: 02/08/2023] Open
Abstract
Synthetic biology, genome engineering and directed evolution offer innumerable tools to expedite engineering of strains for optimising biosynthetic pathways. One of the most radical is SCRaMbLE, a system of inducible in vivo deletion and rearrangement of synthetic yeast chromosomes, diversifying the genotype of millions of Saccharomyces cerevisiae cells in hours. SCRaMbLE can yield strains with improved biosynthetic phenotypes but is limited by screening capabilities. To address this bottleneck, we combine automated sample preparation, an ultra-fast 84-second LC-MS method, and barcoded nanopore sequencing to rapidly isolate and characterise the best performing strains. Here, we use SCRaMbLE to optimise yeast strains engineered to produce the triterpenoid betulinic acid. Our semi-automated workflow screens 1,000 colonies, identifying and sequencing 12 strains with between 2- to 7-fold improvement in betulinic acid titre. The broad applicability of this workflow to rapidly isolate improved strains from a variant library makes this a valuable tool for biotechnology.
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Affiliation(s)
- G-O F Gowers
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - S M Chee
- London Biofoundry, Imperial College London, London, SW7 2AZ, UK
- SynbiCITE, Imperial College London, London, SW7 2AZ, UK
| | - D Bell
- London Biofoundry, Imperial College London, London, SW7 2AZ, UK
- SynbiCITE, Imperial College London, London, SW7 2AZ, UK
- Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - L Suckling
- London Biofoundry, Imperial College London, London, SW7 2AZ, UK
- SynbiCITE, Imperial College London, London, SW7 2AZ, UK
- Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - M Kern
- GlaxoSmithKline, Stevenage, SG1 2NY, UK
| | - D Tew
- GlaxoSmithKline, Stevenage, SG1 2NY, UK
| | - D W McClymont
- London Biofoundry, Imperial College London, London, SW7 2AZ, UK
- SynbiCITE, Imperial College London, London, SW7 2AZ, UK
| | - T Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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30
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Vavricka CJ, Hasunuma T, Kondo A. Dynamic Metabolomics for Engineering Biology: Accelerating Learning Cycles for Bioproduction. Trends Biotechnol 2020; 38:68-82. [DOI: 10.1016/j.tibtech.2019.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 12/15/2022]
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Venayak N, Raj K, Mahadevan R. Impact framework: A python package for writing data analysis workflows to interpret microbial physiology. Metab Eng Commun 2019; 9:e00089. [PMID: 31011536 PMCID: PMC6462781 DOI: 10.1016/j.mec.2019.e00089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 12/26/2022] Open
Abstract
Microorganisms can be genetically engineered to solve a range of challenges in diverse including health, environmental protection and sustainability. The natural complexity of biological systems makes this an iterative cycle, perturbing metabolism and making stepwise progress toward a desired phenotype through four major stages: design, build, test, and data interpretation. This cycle has been accelerated by advances in molecular biology (e.g. robust DNA synthesis and assembly techniques), liquid handling automation and scale-down characterization platforms, generating large heterogeneous data sets. Here, we present an extensible Python package for scientists and engineers working with large biological data sets to interpret, model, and visualize data: the IMPACT (Integrated Microbial Physiology: Analysis, Characterization and Translation) framework. Impact aims to ease the development of Python-based data analysis workflows for a range of stakeholders in the bioengineering process, offering open-source tools for data analysis, physiology characterization and translation to visualization. Using this framework, biologists and engineers can opt for reproducible and extensible programmatic data analysis workflows, mediating a bottleneck limiting the throughput of microbial engineering. The Impact framework is available at https://github.com/lmse/impact.
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Affiliation(s)
- Naveen Venayak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Kaushik Raj
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
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32
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Gowers GOF, Cameron SJS, Perdones-Montero A, Bell D, Chee SM, Kern M, Tew D, Ellis T, Takáts Z. Off-Colony Screening of Biosynthetic Libraries by Rapid Laser-Enabled Mass Spectrometry. ACS Synth Biol 2019; 8:2566-2575. [PMID: 31622554 DOI: 10.1021/acssynbio.9b00243] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
By leveraging advances in DNA synthesis and molecular cloning techniques, synthetic biology increasingly makes use of large construct libraries to explore large design spaces. For biosynthetic pathway engineering, the ability to screen these libraries for a variety of metabolites of interest is essential. If the metabolite of interest or the metabolic phenotype is not easily measurable, screening soon becomes a major bottleneck involving time-consuming culturing, sample preparation, and extraction. To address this, we demonstrate the use of automated laser-assisted rapid evaporative ionization mass spectrometry (LA-REIMS)-a form of ambient laser desorption ionization mass spectrometry-to perform rapid mass spectrometry analysis direct from agar plate yeast colonies without sample preparation or extraction. We use LA-REIMS to assess production levels of violacein and betulinic acid directly from yeast colonies at a rate of 6 colonies per minute. We then demonstrate the throughput enabled by LA-REIMS by screening over 450 yeast colonies within <4 h, while simultaneously generating recoverable glycerol stocks of each colony in real time. This showcases LA-REIMS as a prescreening tool to complement downstream quantification methods such as liquid chromatography-mass spectroscopy (LCMS). By prescreening several hundred colonies with LA-REIMS, we successfully isolate and verify a strain with a 2.5-fold improvement in betulinic acid production. Finally, we show that LA-REIMS can detect 20 out of a panel of 27 diverse biological molecules, demonstrating the broad applicability of LA-REIMS to metabolite detection. The rapid and automated nature of LA-REIMS makes this a valuable new technology to complement existing screening technologies currently employed in academic and industrial workflows.
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Affiliation(s)
- Glen-Oliver F. Gowers
- Imperial College Centre for Synthetic Biology (IC−CSynB), Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Simon J. S. Cameron
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
- Ambimass, London W12 0BZ, United Kingdom
| | - Alvaro Perdones-Montero
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
- Ambimass, London W12 0BZ, United Kingdom
| | - David Bell
- SynbiCITE, Imperial College London, London SW7 2AZ, United Kingdom
| | - Soo Mei Chee
- SynbiCITE, Imperial College London, London SW7 2AZ, United Kingdom
| | - Marcelo Kern
- GlaxoSmithKline, Stevenage SG1 2NY, United Kingdom
| | - David Tew
- GlaxoSmithKline, Stevenage SG1 2NY, United Kingdom
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology (IC−CSynB), Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Zoltan Takáts
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
- Ambimass, London W12 0BZ, United Kingdom
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Thompson MG, Costello Z, Hummel NFC, Cruz-Morales P, Blake-Hedges JM, Krishna RN, Skyrud W, Pearson AN, Incha MR, Shih PM, Garcia-Martin H, Keasling JD. Robust Characterization of Two Distinct Glutarate Sensing Transcription Factors of Pseudomonas putida l-Lysine Metabolism. ACS Synth Biol 2019; 8:2385-2396. [PMID: 31518500 DOI: 10.1021/acssynbio.9b00255] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A significant bottleneck in synthetic biology involves screening large genetically encoded libraries for desirable phenotypes such as chemical production. However, transcription factor-based biosensors can be leveraged to screen thousands of genetic designs for optimal chemical production in engineered microbes. In this study we characterize two glutarate sensing transcription factors (CsiR and GcdR) from Pseudomonas putida. The genomic contexts of csiR homologues were analyzed, and their DNA binding sites were bioinformatically predicted. Both CsiR and GcdR were purified and shown to bind upstream of their coding sequencing in vitro. CsiR was shown to dissociate from DNA in vitro when exogenous glutarate was added, confirming that it acts as a genetic repressor. Both transcription factors and cognate promoters were then cloned into broad host range vectors to create two glutarate biosensors. Their respective sensing performance features were characterized, and more sensitive derivatives of the GcdR biosensor were created by manipulating the expression of the transcription factor. Sensor vectors were then reintroduced into P. putida and evaluated for their ability to respond to glutarate and various lysine metabolites. Additionally, we developed a novel mathematical approach to describe the usable range of detection for genetically encoded biosensors, which may be broadly useful in future efforts to better characterize biosensor performance.
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Affiliation(s)
- Mitchell G. Thompson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Zak Costello
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Niklas F. C. Hummel
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Department of Plant Biology, University of California, Davis, Davis, California 95616, United States
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Centro de Biotecnologia FEMSA, Instituto Tecnologico y de Estudios Superiores de Monterrey, 64849 Monterrey, Mexico
| | - Jacquelyn M. Blake-Hedges
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Rohith N. Krishna
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Will Skyrud
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Allison N. Pearson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Matthew R. Incha
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Patrick M. Shih
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Department of Plant Biology, University of California, Davis, Davis, California 95616, United States
| | - Hector Garcia-Martin
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- BCAM, Basque Center for Applied Mathematics, 48009 Bilbao, Spain
| | - Jay D. Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Program in Bioengineering, University of California, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Synthetic biology industry: data-driven design is creating new opportunities in biotechnology. Emerg Top Life Sci 2019; 3:651-657. [PMID: 33523172 PMCID: PMC7289019 DOI: 10.1042/etls20190040] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 01/09/2023]
Abstract
Synthetic biology is a rapidly emerging interdisciplinary research field that is primarily built upon foundational advances in molecular biology combined with engineering design. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies. This has spurned a rapid growth in start-up companies and the new synthetic biology industry is growing rapidly, with start-up companies receiving ∼$6.1B investment since 2015 and a global synthetic biology market value estimated to be $14B by 2026. Many of the new start-ups can be grouped within a multi-layer ‘technology stack’. The ‘stack’ comprises a number of technology layers which together can be applied to a diversity of new biotechnology applications like consumer biotechnology products and living therapies. The ‘stack’ also enables new commercial opportunities and value chains similar to the software design and manufacturing revolution of the 20th century. However, the synthetic biology industry is at a crucial point, as it now requires recognisable commercial successes in order for the industry to expand and scale, in terms of investment and companies. However, such expansion may directly challenge the ethos of synthetic biology, in terms of open technology sharing and democratisation, which could unintentionally lead to multi-national corporations and technology monopolies similar to the existing biotechnology/biopharma industry.
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35
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Mixed-mode liquid chromatography for the rapid analysis of biocatalytic glucaric acid reaction pathways. Anal Chim Acta 2019; 1066:136-145. [DOI: 10.1016/j.aca.2019.03.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 01/25/2023]
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36
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López J, Cataldo VF, Peña M, Saa PA, Saitua F, Ibaceta M, Agosin E. Build Your Bioprocess on a Solid Strain-β-Carotene Production in Recombinant Saccharomyces cerevisiae. Front Bioeng Biotechnol 2019; 7:171. [PMID: 31380362 PMCID: PMC6656860 DOI: 10.3389/fbioe.2019.00171] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/03/2019] [Indexed: 11/19/2022] Open
Abstract
Robust fermentation performance of microbial cell factories is critical for successful scaling of a biotechnological process. From shake flask cultivations to industrial-scale bioreactors, consistent strain behavior is fundamental to achieve the production targets. To assert the importance of this feature, we evaluated the impact of the yeast strain design and construction method on process scalability -from shake flasks to bench-scale fed-batch fermentations- using two recombinant Saccharomyces cerevisiae strains capable of producing β-carotene; SM14 and βcar1.2 strains. SM14 strain, obtained previously from adaptive evolution experiments, was capable to accumulate up to 21 mg/gDCW of β-carotene in 72 h shake flask cultures; while the βcar1.2, constructed by overexpression of carotenogenic genes, only accumulated 5.8 mg/gDCW of carotene. Surprisingly, fed-batch cultivation of these strains in 1L bioreactors resulted in opposite performances. βcar1.2 strain reached much higher biomass and β-carotene productivities (1.57 g/L/h and 10.9 mg/L/h, respectively) than SM14 strain (0.48 g/L/h and 3.1 mg/L/h, respectively). Final β-carotene titers were 210 and 750 mg/L after 80 h cultivation for SM14 and βcar1.2 strains, respectively. Our results indicate that these substantial differences in fermentation parameters are mainly a consequence of the exacerbated Crabtree effect of the SM14 strain. We also found that the strategy used to integrate the carotenogenic genes into the chromosomes affected the genetic stability of strains, although the impact was significantly minor. Overall, our results indicate that shake flasks fermentation parameters are poor predictors of the fermentation performance under industrial-like conditions, and that appropriate construction designs and performance tests must be conducted to properly assess the scalability of the strain and the bioprocess.
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Affiliation(s)
- Javiera López
- Centro de Aromas and Sabores, DICTUC S.A., Santiago, Chile.,Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Vicente F Cataldo
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Manuel Peña
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pedro A Saa
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Maximiliano Ibaceta
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eduardo Agosin
- Centro de Aromas and Sabores, DICTUC S.A., Santiago, Chile.,Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
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St. John PC, Bomble YJ. Approaches to Computational Strain Design in the Multiomics Era. Front Microbiol 2019; 10:597. [PMID: 31024467 PMCID: PMC6461008 DOI: 10.3389/fmicb.2019.00597] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/08/2019] [Indexed: 01/29/2023] Open
Abstract
Modern omics analyses are able to effectively characterize the genetic, regulatory, and metabolic phenotypes of engineered microbes, yet designing genetic interventions to achieve a desired phenotype remains challenging. With recent developments in genetic engineering techniques, timelines associated with building and testing strain designs have been greatly reduced, allowing for the first time an efficient closed loop iteration between experiment and analysis. However, the scale and complexity associated with multi-omics datasets complicates manual biological reasoning about the mechanisms driving phenotypic changes. Computational techniques therefore form a critical part of the Design-Build-Test-Learn (DBTL) cycle in metabolic engineering. Traditional statistical approaches can reduce the dimensionality of these datasets and identify common motifs among high-performing strains. While successful in many studies, these methods do not take full advantage of known connections between genes, proteins, and metabolic networks. There is therefore a growing interest in model-aided design, in which modeling frameworks from systems biology are used to integrate experimental data and generate effective and non-intuitive design predictions. In this mini-review, we discuss recent progress and challenges in this field. In particular, we compare methods augmenting flux balance analysis with additional constraints from fluxomic, genomic, and metabolomic datasets and methods employing kinetic representations of individual metabolic reactions, and machine learning. We conclude with a discussion of potential future directions for improving strain design predictions in the omics era and remaining experimental and computational hurdles.
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Morelli L, Centorbi FA, Ilchenko O, Jendresen CB, Demarchi D, Nielsen AT, Zór K, Boisen A. Simultaneous quantification of multiple bacterial metabolites using surface-enhanced Raman scattering. Analyst 2019; 144:1600-1607. [DOI: 10.1039/c8an02128g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We combine liquid–liquid extraction, SERS detection and partial least squares analysis for simultaneous quantification of bacterial metabolites in E. coli supernatant.
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Affiliation(s)
- Lidia Morelli
- Department of Micro- and Nanotechnology
- Technical University of Denmark
- Denmark
| | | | - Oleksii Ilchenko
- Department of Micro- and Nanotechnology
- Technical University of Denmark
- Denmark
| | | | - Danilo Demarchi
- Department of Electronics and Telecommunications
- 10129 Torino
- Italy
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability
- Technical University of Denmark
- Denmark
| | - Kinga Zór
- Department of Micro- and Nanotechnology
- Technical University of Denmark
- Denmark
| | - Anja Boisen
- Department of Micro- and Nanotechnology
- Technical University of Denmark
- Denmark
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39
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Becker J, Wittmann C. From systems biology to metabolically engineered cells — an omics perspective on the development of industrial microbes. Curr Opin Microbiol 2018; 45:180-188. [DOI: 10.1016/j.mib.2018.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/06/2018] [Accepted: 06/08/2018] [Indexed: 10/28/2022]
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40
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Abstract
Population growth, climate change, and dwindling finite resources are amongst the major challenges which are facing the planet. Requirements for food, materials, water, and energy will soon exceed capacity. Green biotechnology, fueled by recent plant synthetic biology breakthroughs, may offer solutions. This review summarizes current progress towards robust and predictable engineering of plants. I then discuss applications from the lab and field, with a focus on bioenergy, biomaterials, and medicine.
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Affiliation(s)
- Jenny C Mortimer
- 1 Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,2 Joint BioEnergy Institute, Emeryville, CA 94608, USA
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41
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Tokic M, Hadadi N, Ataman M, Neves D, Ebert BE, Blank LM, Miskovic L, Hatzimanikatis V. Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors. ACS Synth Biol 2018; 7:1858-1873. [PMID: 30021444 DOI: 10.1021/acssynbio.8b00049] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The limited supply of fossil fuels and the establishment of new environmental policies shifted research in industry and academia toward sustainable production of the second generation of biofuels, with methyl ethyl ketone (MEK) being one promising fuel candidate. MEK is a commercially valuable petrochemical with an extensive application as a solvent. However, as of today, a sustainable and economically viable production of MEK has not yet been achieved despite several attempts of introducing biosynthetic pathways in industrial microorganisms. We used BNICE.ch as a retrobiosynthesis tool to discover all novel pathways around MEK. Out of 1325 identified compounds connecting to MEK with one reaction step, we selected 3-oxopentanoate, but-3-en-2-one, but-1-en-2-olate, butylamine, and 2-hydroxy-2-methylbutanenitrile for further study. We reconstructed 3 679 610 novel biosynthetic pathways toward these 5 compounds. We then embedded these pathways into the genome-scale model of E. coli, and a set of 18 622 were found to be the most biologically feasible ones on the basis of thermodynamics and their yields. For each novel reaction in the viable pathways, we proposed the most similar KEGG reactions, with their gene and protein sequences, as candidates for either a direct experimental implementation or as a basis for enzyme engineering. Through pathway similarity analysis we classified the pathways and identified the enzymes and precursors that were indispensable for the production of the target molecules. These retrobiosynthesis studies demonstrate the potential of BNICE.ch for discovery, systematic evaluation, and analysis of novel pathways in synthetic biology and metabolic engineering studies.
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Affiliation(s)
- Milenko Tokic
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Noushin Hadadi
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Meric Ataman
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Dário Neves
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, D-52056 Aachen, Germany
| | - Birgitta E. Ebert
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, D-52056 Aachen, Germany
| | - Lars M. Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, D-52056 Aachen, Germany
| | - Ljubisa Miskovic
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
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42
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Halbfeld C, Baumbach JI, Blank LM, Ebert BE. Multi-capillary Column Ion Mobility Spectrometry of Volatile Metabolites for Phenotyping of Microorganisms. Methods Mol Biol 2018; 1671:229-258. [PMID: 29170963 DOI: 10.1007/978-1-4939-7295-1_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Rational strain engineering requires solid testing of phenotypes including productivity and ideally contributes thereby directly to our understanding of the genotype-phenotype relationship. Actually, the test step of the strain engineering cycle becomes the limiting step, as ever advancing tools for generating genetic diversity exist. Here, we briefly define the challenge one faces in quantifying phenotypes and summarize existing analytical techniques that partially overcome this challenge. We argue that the evolution of volatile metabolites can be used as proxy for cellular metabolism. In the simplest case, the product of interest is a volatile (e.g., from bulk alcohols to special fragrances) that is directly quantified over time. But also nonvolatile products (e.g., from bulk long-chain fatty acids to natural products) require major flux rerouting that result potentially in altered volatile production. While alternative techniques for volatile determination exist, rather few can be envisaged for medium to high-throughput analysis required for phenotype testing. Here, we contribute a detailed protocol for an ion mobility spectrometry (IMS) analysis that allows volatile metabolite quantification down to the ppb range. The sensitivity can be exploited for small-scale fermentation monitoring. The insights shared might contribute to a more frequent use of IMS in biotechnology, while the experimental aspects are of general use for researchers interested in volatile monitoring.
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Affiliation(s)
- Christoph Halbfeld
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
| | - Jörg Ingo Baumbach
- Faculty of Applied Chemistry, Reutlingen University, 72762, Reutlingen, Germany
| | - Lars M Blank
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany.
| | - Birgitta E Ebert
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
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Ye K, Kaplan DL, Bao G, Bettinger C, Forgacs G, Dong C, Khademhosseini A, Ke Y, Leong K, Sambanis A, Sun W, Yin P. Advanced Cell and Tissue Biomanufacturing. ACS Biomater Sci Eng 2018; 4:2292-2307. [PMID: 33435095 DOI: 10.1021/acsbiomaterials.8b00650] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This position paper assesses state-of-the-art advanced biomanufacturing and identifies paths forward to advance this emerging field in biotechnology and biomedical engineering, including new research opportunities and translational and corporate activities. The vision for the field is to see advanced biomanufacturing emerge as a discipline in academic and industrial communities as well as a technological opportunity to spur research and industry growth. To navigate this vision, the paths to move forward and to identify major barriers were a focal point of discussions at a National Science Foundation-sponsored workshop focused on the topic. Some of the major needs include but are not limited to the integration of specific scientific and engineering disciplines and guidance from regulatory agencies, infrastructure requirements, and strategies for reliable systems integration. Some of the recommendations, major targets, and opportunities were also outlined, including some "grand challenges" to spur interest and progress in the field based on the participants at the workshop. Many of these recommendations have been expanded, materialized, and adopted by the field. For instance, the formation of an initial collaboration network in the community was established. This report provides suggestions for the opportunities and challenges to help move the field of advanced biomanufacturing forward. The field is in the early stages of effecting science and technology in biomanufacturing with a bright and important future impact evident based on the rapid scientific advances in recent years and industry progress.
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Affiliation(s)
- Kaiming Ye
- Department of Biomedical Engineering, Center of Biomanufacturing for Regenerative Medicine, Watson School of Engineering and Applied Science, Binghamton University, State University of New York (SUNY), Binghamton, New York 13902, United States
| | - David L Kaplan
- Department of Biomedical Engineering, School of Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Gang Bao
- Department of Bioengineering, School of Engineering, Rice University, Houston, Texas 77005, United States
| | - Christopher Bettinger
- Department of Materials Science and Engineering, College of Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Gabor Forgacs
- Department of Bioengineering, College of Engineering, University of Missouri, Columbia, Missouri 65211, United States.,Modern Meadow, Inc., 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Cheng Dong
- Department of Biomedical Engineering, College of Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Ali Khademhosseini
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Yonggang Ke
- Department of Biomedical Engineering, College of Engineering, Georgia Tech, Atlanta, Georgia 30332, United States
| | - Kam Leong
- Department of Biomedical Engineering, School of Engineering and Applied Science, Columbia University, New York City, New York 10027, United States
| | | | - Wei Sun
- Department of Mechanical Engineering and Mechanics, College of Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States.,Department of Mechanical Engineering, Tsinghua University, Beijing, China
| | - Peng Yin
- Department of Systems Biology, Harvard Medical School, Cambridge, Massachusetts 02138, United States
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44
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Basu S, Rabara RC, Negi S, Shukla P. Engineering PGPMOs through Gene Editing and Systems Biology: A Solution for Phytoremediation? Trends Biotechnol 2018; 36:499-510. [DOI: 10.1016/j.tibtech.2018.01.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 01/17/2023]
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45
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Sardi M, Gasch AP. Incorporating comparative genomics into the design-test-learn cycle of microbial strain engineering. FEMS Yeast Res 2018. [PMID: 28637316 DOI: 10.1093/femsyr/fox042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Engineering microbes with new properties is an important goal in industrial engineering, to establish biological factories for production of biofuels, commodity chemicals and pharmaceutics. But engineering microbes to produce new compounds with high yield remains a major challenge toward economically viable production. Incorporating several modern approaches, including synthetic and systems biology, metabolic modeling and regulatory rewiring, has proven to significantly advance industrial strain engineering. This review highlights how comparative genomics can also facilitate strain engineering, by identifying novel genes and pathways, regulatory mechanisms and genetic background effects for engineering. We discuss how incorporating comparative genomics into the design-test-learn cycle of strain engineering can provide novel information that complements other engineering strategies.
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Affiliation(s)
- Maria Sardi
- Great Lakes Bioenergy Research Center, Madison, WI 53706, USA
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, Madison, WI 53706, USA.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
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46
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In situ biomolecule production by bacteria; a synthetic biology approach to medicine. J Control Release 2018; 275:217-228. [DOI: 10.1016/j.jconrel.2018.02.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 02/06/2023]
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47
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RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H. BMC Genomics 2018; 19:24. [PMID: 29304737 PMCID: PMC5756330 DOI: 10.1186/s12864-017-4415-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 12/22/2017] [Indexed: 01/05/2023] Open
Abstract
Background The acetic acid bacterium Gluconobacter oxydans 621H is characterized by its exceptional ability to incompletely oxidize a great variety of carbohydrates in the periplasm. The metabolism of this α-proteobacterium has been characterized to some extent, yet little is known about its transcriptomes and related data. In this study, we applied two different RNAseq approaches. Primary transcriptomes enriched for 5′-ends of transcripts were sequenced to detect transcription start sites, which allow subsequent analysis of promoter motifs, ribosome binding sites, and 5´-UTRs. Whole transcriptomes were sequenced to identify expressed genes and operon structures. Results Sequencing of primary transcriptomes of G. oxydans revealed 2449 TSSs, which were classified according to their genomic context followed by identification of promoter and ribosome binding site motifs, analysis of 5´-UTRs including validation of predicted cis-regulatory elements and correction of start codons. 1144 (41%) of all genes were found to be expressed monocistronically, whereas 1634 genes were organized in 571 operons. Together, TSSs and whole transcriptome data were also used to identify novel intergenic (18), intragenic (328), and antisense transcripts (313). Conclusions This study provides deep insights into the transcriptional landscapes of G. oxydans. The comprehensive transcriptome data, which we made publicly available, facilitate further analysis of promoters and other regulatory elements. This will support future approaches for rational strain development and targeted gene expression in G. oxydans. The corrections of start codons further improve the high quality genome reference and support future proteome analysis. Electronic supplementary material The online version of this article (10.1186/s12864-017-4415-x) contains supplementary material, which is available to authorized users.
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48
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Engineering of global regulators and cell surface properties toward enhancing stress tolerance in Saccharomyces cerevisiae. J Biosci Bioeng 2017; 124:599-605. [DOI: 10.1016/j.jbiosc.2017.06.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 01/22/2023]
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49
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Development of a high-performance, enterprise-level, multimode LC–MS/MS autosampler for drug discovery. Bioanalysis 2017; 9:1643-1654. [DOI: 10.4155/bio-2017-0149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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50
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Kim SM, Peña MI, Moll M, Bennett GN, Kavraki LE. A review of parameters and heuristics for guiding metabolic pathfinding. J Cheminform 2017; 9:51. [PMID: 29086092 PMCID: PMC5602787 DOI: 10.1186/s13321-017-0239-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/07/2017] [Indexed: 12/04/2022] Open
Abstract
Recent developments in metabolic engineering have led to the successful biosynthesis of valuable products, such as the precursor of the antimalarial compound, artemisinin, and opioid precursor, thebaine. Synthesizing these traditionally plant-derived compounds in genetically modified yeast cells introduces the possibility of significantly reducing the total time and resources required for their production, and in turn, allows these valuable compounds to become cheaper and more readily available. Most biosynthesis pathways used in metabolic engineering applications have been discovered manually, requiring a tedious search of existing literature and metabolic databases. However, the recent rapid development of available metabolic information has enabled the development of automated approaches for identifying novel pathways. Computer-assisted pathfinding has the potential to save biochemists time in the initial discovery steps of metabolic engineering. In this paper, we review the parameters and heuristics used to guide the search in recent pathfinding algorithms. These parameters and heuristics capture information on the metabolic network structure, compound structures, reaction features, and organism-specificity of pathways. No one metabolic pathfinding algorithm or search parameter stands out as the best to use broadly for solving the pathfinding problem, as each method and parameter has its own strengths and shortcomings. As assisted pathfinding approaches continue to become more sophisticated, the development of better methods for visualizing pathway results and integrating these results into existing metabolic engineering practices is also important for encouraging wider use of these pathfinding methods.
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Affiliation(s)
- Sarah M Kim
- Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Matthew I Peña
- Department of BioSciences, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Mark Moll
- Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - George N Bennett
- Department of BioSciences, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Lydia E Kavraki
- Department of Computer Science, Rice University, 6100 Main St., Houston, TX, 77005, USA.
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