1
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Böhm C, Inckemann R, Burgis M, Baumann J, Brinkmann CK, Lipinska KE, Gilles S, Freudigmann J, Seiler VN, Clark LG, Jewett MC, Voll LM, Niederholtmeyer H. Chloroplast Cell-Free Systems from Different Plant Species as a Rapid Prototyping Platform. ACS Synth Biol 2024; 13:2412-2424. [PMID: 39028299 PMCID: PMC11334176 DOI: 10.1021/acssynbio.4c00117] [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: 02/19/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 07/20/2024]
Abstract
Climate change poses a significant threat to global agriculture, necessitating innovative solutions. Plant synthetic biology, particularly chloroplast engineering, holds promise as a viable approach to this challenge. Chloroplasts present a variety of advantageous traits for genetic engineering, but the development of genetic tools and genetic part characterization in these organelles is hindered by the lengthy time scales required to generate transplastomic organisms. To address these challenges, we have established a versatile protocol for generating highly active chloroplast-based cell-free gene expression (CFE) systems derived from a diverse range of plant species, including wheat (monocot), spinach, and poplar trees (dicots). We show that these systems work with conventionally used T7 RNA polymerase as well as the endogenous chloroplast polymerases, allowing for detailed characterization and prototyping of regulatory sequences at both transcription and translation levels. To demonstrate the platform for characterization of promoters and 5' and 3' untranslated regions (UTRs) in higher plant chloroplast gene expression, we analyze a collection of 23 5'UTRs, 10 3'UTRs, and 6 chloroplast promoters, assessed their expression in spinach and wheat extracts, and found consistency in expression patterns, suggesting cross-species compatibility. Looking forward, our chloroplast CFE systems open new avenues for plant synthetic biology, offering prototyping tools for both understanding gene expression and developing engineered plants, which could help meet the demands of a changing global climate.
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Affiliation(s)
- Clemens
V. Böhm
- Max-Planck
Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
| | - René Inckemann
- Max-Planck
Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
| | - Michael Burgis
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
| | - Jessica Baumann
- Molecular
Plant Physiology, Philipps-Universität
Marburg, 35043 Marburg, Germany
| | | | - Katarzyna E. Lipinska
- Max-Planck
Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
| | - Sara Gilles
- Max-Planck
Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
| | - Jonas Freudigmann
- Molecular
Plant Physiology, Philipps-Universität
Marburg, 35043 Marburg, Germany
| | - Vinca N. Seiler
- Molecular
Plant Physiology, Philipps-Universität
Marburg, 35043 Marburg, Germany
| | - Lauren G. Clark
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Lars M. Voll
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
- Molecular
Plant Physiology, Philipps-Universität
Marburg, 35043 Marburg, Germany
| | - Henrike Niederholtmeyer
- Max-Planck
Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-Universität
Marburg, 35032 Marburg, Germany
- Technical
University of Munich, Campus Straubing for Biotechnology and Sustainability, 94315 Straubing, Germany
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2
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Aspacio D, Zhang Y, Cui Y, Luu E, King E, Black WB, Perea S, Zhu Q, Wu Y, Luo R, Siegel JB, Li H. Shifting redox reaction equilibria on demand using an orthogonal redox cofactor. Nat Chem Biol 2024:10.1038/s41589-024-01702-5. [PMID: 39138383 DOI: 10.1038/s41589-024-01702-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 07/16/2024] [Indexed: 08/15/2024]
Abstract
Nature's two redox cofactors, nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), are held at different reduction potentials, driving catabolism and anabolism in opposite directions. In biomanufacturing, there is a need to flexibly control redox reaction direction decoupled from catabolism and anabolism. We established nicotinamide mononucleotide (NMN+) as a noncanonical cofactor orthogonal to NAD(P)+. Here we present the development of Nox Ortho, a reduced NMN+ (NMNH)-specific oxidase, that completes the toolkit to modulate NMNH:NMN+ ratio together with an NMN+-specific glucose dehydrogenase (GDH Ortho). The design principle discovered from Nox Ortho engineering and modeling is facilely translated onto six different enzymes to create NMN(H)-orthogonal biocatalysts with a consistent ~103-106-fold cofactor specificity switch from NAD(P)+ to NMN+. We assemble these enzymes to produce stereo-pure 2,3-butanediol in cell-free systems and in Escherichia coli, enabled by NMN(H)'s distinct redox ratio firmly set by its designated driving forces, decoupled from both NAD(H) and NADP(H).
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Affiliation(s)
- Derek Aspacio
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Yulai Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Youtian Cui
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Emma Luu
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - William B Black
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Sean Perea
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Qiang Zhu
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
- Department of Material Science and Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Yongxian Wu
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
- Department of Material Science and Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Ray Luo
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
- Department of Material Science and Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Justin B Siegel
- Genome Center, University of California, Davis, Davis, CA, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA.
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA.
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA.
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3
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Cardiff RAL, Carothers JM, Zalatan JG, Sauro HM. Systems-Level Modeling for CRISPR-Based Metabolic Engineering. ACS Synth Biol 2024. [PMID: 39119666 DOI: 10.1021/acssynbio.4c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
The CRISPR-Cas system has enabled the development of sophisticated, multigene metabolic engineering programs through the use of guide RNA-directed activation or repression of target genes. To optimize biosynthetic pathways in microbial systems, we need improved models to inform design and implementation of transcriptional programs. Recent progress has resulted in new modeling approaches for identifying gene targets and predicting the efficacy of guide RNA targeting. Genome-scale and flux balance models have successfully been applied to identify targets for improving biosynthetic production yields using combinatorial CRISPR-interference (CRISPRi) programs. The advent of new approaches for tunable and dynamic CRISPR activation (CRISPRa) promises to further advance these engineering capabilities. Once appropriate targets are identified, guide RNA prediction models can lead to increased efficacy in gene targeting. Developing improved models and incorporating approaches from machine learning may be able to overcome current limitations and greatly expand the capabilities of CRISPR-Cas9 tools for metabolic engineering.
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Affiliation(s)
- Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - James M Carothers
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jesse G Zalatan
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Herbert M Sauro
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
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4
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Burbano DA, Kiattisewee C, Karanjia AV, Cardiff RAL, Faulkner ID, Sugianto W, Carothers JM. CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications. Annu Rev Chem Biomol Eng 2024; 15:389-430. [PMID: 38598861 DOI: 10.1146/annurev-chembioeng-100522-114706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
In the past decades, the broad selection of CRISPR-Cas systems has revolutionized biotechnology by enabling multimodal genetic manipulation in diverse organisms. Rooted in a molecular engineering perspective, we recapitulate the different CRISPR components and how they can be designed for specific genetic engineering applications. We first introduce the repertoire of Cas proteins and tethered effectors used to program new biological functions through gene editing and gene regulation. We review current guide RNA (gRNA) design strategies and computational tools and how CRISPR-based genetic circuits can be constructed through regulated gRNA expression. Then, we present recent advances in CRISPR-based biosensing, bioproduction, and biotherapeutics across in vitro and in vivo prokaryotic systems. Finally, we discuss forthcoming applications in prokaryotic CRISPR technology that will transform synthetic biology principles in the near future.
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Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Cholpisit Kiattisewee
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ava V Karanjia
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ian D Faulkner
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - James M Carothers
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
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5
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Boob AG, Chen J, Zhao H. Enabling pathway design by multiplex experimentation and machine learning. Metab Eng 2024; 81:70-87. [PMID: 38040110 DOI: 10.1016/j.ymben.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/01/2023] [Accepted: 11/25/2023] [Indexed: 12/03/2023]
Abstract
The remarkable metabolic diversity observed in nature has provided a foundation for sustainable production of a wide array of valuable molecules. However, transferring the biosynthetic pathway to the desired host often runs into inherent failures that arise from intermediate accumulation and reduced flux resulting from competing pathways within the host cell. Moreover, the conventional trial and error methods utilized in pathway optimization struggle to fully grasp the intricacies of installed pathways, leading to time-consuming and labor-intensive experiments, ultimately resulting in suboptimal yields. Considering these obstacles, there is a pressing need to explore the enzyme expression landscape and identify the optimal pathway configuration for enhanced production of molecules. This review delves into recent advancements in pathway engineering, with a focus on multiplex experimentation and machine learning techniques. These approaches play a pivotal role in overcoming the limitations of traditional methods, enabling exploration of a broader design space and increasing the likelihood of discovering optimal pathway configurations for enhanced production of molecules. We discuss several tools and strategies for pathway design, construction, and optimization for sustainable and cost-effective microbial production of molecules ranging from bulk to fine chemicals. We also highlight major successes in academia and industry through compelling case studies.
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Affiliation(s)
- Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Junyu Chen
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.
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6
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Yi X, Rasor BJ, Boadi N, Louie K, Northen TR, Karim AS, Jewett MC, Alper HS. Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping. Metab Eng 2023; 80:241-253. [PMID: 37890611 DOI: 10.1016/j.ymben.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/07/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
Building and optimizing biosynthetic pathways in engineered cells holds promise to address societal needs in energy, materials, and medicine, but it is often time-consuming. Cell-free synthetic biology has emerged as a powerful tool to accelerate design-build-test-learn cycles for pathway engineering with increased tolerance to toxic compounds. However, most cell-free pathway prototyping to date has been performed in extracts from wildtype cells which often do not have sufficient flux towards the pathways of interest, which can be enhanced by engineering. Here, to address this gap, we create a set of engineered Escherichia coli and Saccharomyces cerevisiae strains rewired via CRISPR-dCas9 to achieve high-flux toward key metabolic precursors; namely, acetyl-CoA, shikimate, triose-phosphate, oxaloacetate, α-ketoglutarate, and glucose-6-phosphate. Cell-free extracts generated from these strains are used for targeted enzyme screening in vitro. As model systems, we assess in vivo and in vitro production of triacetic acid lactone from acetyl-CoA and muconic acid from the shikimate pathway. The need for these platforms is exemplified by the fact that muconic acid cannot be detected in wildtype extracts provided with the same biosynthetic enzymes. We also perform metabolomic comparison to understand biochemical differences between the cellular and cell-free muconic acid synthesis systems (E. coli and S. cerevisiae cells and cell extracts with and without metabolic rewiring). While any given pathway has different interfaces with metabolism, we anticipate that this set of pre-optimized, flux enhanced cell extracts will enable prototyping efforts for new biosynthetic pathways and the discovery of biochemical functions of enzymes.
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Affiliation(s)
- Xiunan Yi
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA; McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Nathalie Boadi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Katherine Louie
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent R Northen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA; Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA; McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA.
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7
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Aspacio D, Zhang Y, Cui Y, King E, Black WB, Perea S, Luu E, Siegel JB, Li H. Shifting Redox Reaction Equilibria on Demand Using an Orthogonal Redox Cofactor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555398. [PMID: 37693387 PMCID: PMC10491207 DOI: 10.1101/2023.08.29.555398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Natural metabolism relies on chemical compartmentalization of two redox cofactors, NAD+ and NADP+, to orchestrate life-essential redox reaction directions. However, in whole cells the reliance on these canonical cofactors limits flexible control of redox reaction direction as these reactions are permanently tied to catabolism or anabolism. In cell-free systems, NADP+ is too expensive in large scale. We have previously reported the use of nicotinamide mononucleotide, (NMN+) as a low-cost, noncanonical redox cofactor capable of specific electron delivery to diverse chemistries. Here, we present Nox Ortho, an NMNH-specific water-forming oxidase, that completes the toolkit to modulate NMNH/NMN+ ratio. This work uncovers an enzyme design principle that succeeds in parallel engineering of six butanediol dehydrogenases as NMN(H)-orthogonal biocatalysts consistently with a 103 - 106 -fold cofactor specificity switch from NAD(P)+ to NMN+. We combine these to produce chiral-pure 2,3-butanediol (Bdo) isomers without interference from NAD(H) or NADP(H) in vitro and in E. coli cells. We establish that NMN(H) can be held at a distinct redox ratio on demand, decoupled from both NAD(H) and NADP(H) redox ratios in vitro and in vivo.
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Affiliation(s)
- Derek Aspacio
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Yulai Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Youtian Cui
- Genome Center, University of California, Davis, Davis, California 95616, United States
| | - Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - William B. Black
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Sean Perea
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Emma Luu
- Genome Center, University of California, Davis, Davis, California 95616, United States
| | - Justin B. Siegel
- Genome Center, University of California, Davis, Davis, California 95616, United States
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
- Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
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8
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Liu Y, Zhao Z, Song Y, Yin Y, Wu F, Jiang H. Usage of Cell-Free Protein Synthesis in Post-Translational Modification of μ-Conopeptide PIIIA. Mar Drugs 2023; 21:421. [PMID: 37623702 PMCID: PMC10455749 DOI: 10.3390/md21080421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/20/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023] Open
Abstract
The post-translational modifications of conopeptides are the most complicated modifications to date and are well-known and closely related to the activity of conopeptides. The hydroxylation of proline in conopeptides affects folding, structure, and biological activity, and prolyl 4 hydroxylase has been characterized in Conus literatus. However, the hydroxylation machinery of proline in conopeptides is still unclear. In order to address the hydroxylation mechanism of proline in μ-PIIIA, three recombinant plasmids encoding different hybrid precursors of μ-PIIIA were constructed and crossly combined with protein disulfide isomerase, prolyl 4 hydroxylase, and glutaminyl cyclase in a continuous exchange cell-free protein system. The findings showed that prolyl 4 hydroxylase might recognize the propeptide of μ-PIIIA to achieve the hydroxylation of proline, while the cyclization of glutamate was also formed. Additionally, in Escherichia coli, the co-expression plasmid encoding prolyl 4 hydroxylase and the precursor of μ-PIIIA containing pro and mature regions were used to validate the continuous exchange cell-free protein system. Surprisingly, in addition to the two hydroxyproline residues and one pyroglutamyl residue, three disulfide bridges were formed using Trx as a fusion tag, and the yield of the fusion peptide was approximately 20 mg/L. The results of electrophysiology analysis indicated that the recombinant μ-PIIIA without C-terminal amidate inhibited the current of hNaV1.4 with a 939 nM IC50. Our work solved the issue that it was challenging to quickly generate post-translationally modified conopeptides in vitro. This is the first study to demonstrate that prolyl 4 hydroxylase catalyzes the proline hydroxylation through recognition in the propeptide of μ-PIIIA, and it will provide a new way for synthesizing multi-modified conopeptides with pharmacological activity.
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Affiliation(s)
| | | | | | | | | | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
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9
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Dinglasan JLN, Doktycz MJ. Rewiring cell-free metabolic flux in E. coli lysates using a block-push-pull approach. Synth Biol (Oxf) 2023; 8:ysad007. [PMID: 37908558 PMCID: PMC10615139 DOI: 10.1093/synbio/ysad007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/27/2023] [Accepted: 04/12/2023] [Indexed: 11/02/2023] Open
Abstract
Cell-free systems can expedite the design and implementation of biomanufacturing processes by bypassing troublesome requirements associated with the use of live cells. In particular, the lack of survival objectives and the open nature of cell-free reactions afford engineering approaches that allow purposeful direction of metabolic flux. The use of lysate-based systems to produce desired small molecules can result in competitive titers and productivities when compared to their cell-based counterparts. However, pathway crosstalk within endogenous lysate metabolism can compromise conversion yields by diverting carbon flow away from desired products. Here, the 'block-push-pull' concept of conventional cell-based metabolic engineering was adapted to develop a cell-free approach that efficiently directs carbon flow in lysates from glucose and toward endogenous ethanol synthesis. The approach is readily adaptable, is relatively rapid and allows for the manipulation of central metabolism in cell extracts. In implementing this approach, a block strategy is first optimized, enabling selective enzyme removal from the lysate to the point of eliminating by-product-forming activity while channeling flux through the target pathway. This is complemented with cell-free metabolic engineering methods that manipulate the lysate proteome and reaction environment to push through bottlenecks and pull flux toward ethanol. The approach incorporating these block, push and pull strategies maximized the glucose-to-ethanol conversion in an Escherichia coli lysate that initially had low ethanologenic potential. A 10-fold improvement in the percent yield is demonstrated. To our knowledge, this is the first report of successfully rewiring lysate carbon flux without source strain optimization and completely transforming the consumed input substrate to a desired output product in a lysate-based, cell-free system.
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Affiliation(s)
- Jaime Lorenzo N Dinglasan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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10
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Rasor BJ, Karim AS, Alper HS, Jewett MC. Cell Extracts from Bacteria and Yeast Retain Metabolic Activity after Extended Storage and Repeated Thawing. ACS Synth Biol 2023; 12:904-908. [PMID: 36848582 DOI: 10.1021/acssynbio.2c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Cell-free synthetic biology enables rapid prototyping of biological parts and synthesis of proteins or metabolites in the absence of cell growth constraints. Cell-free systems are frequently made from crude cell extracts, where composition and activity can vary significantly based on source strain, preparation and processing, reagents, and other considerations. This variability can cause extracts to be treated as black boxes for which empirical observations guide practical laboratory practices, including a hesitance to use dated or previously thawed extracts. To better understand the robustness of cell extracts over time, we assessed the activity of cell-free metabolism during storage. As a model, we studied conversion of glucose to 2,3-butanediol. We found that cell extracts from Escherichia coli and Saccharomyces cerevisiae subjected to an 18-month storage period and repeated freeze-thaw cycles retain consistent metabolic activity. This work gives users of cell-free systems a better understanding of the impacts of storage on extract behavior.
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11
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Warfel K, Williams A, Wong DA, Sobol SE, Desai P, Li J, Chang YF, DeLisa MP, Karim AS, Jewett MC. A Low-Cost, Thermostable, Cell-Free Protein Synthesis Platform for On-Demand Production of Conjugate Vaccines. ACS Synth Biol 2022; 12:95-107. [PMID: 36548479 PMCID: PMC9872175 DOI: 10.1021/acssynbio.2c00392] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cell-free protein synthesis systems that can be lyophilized for long-term, non-refrigerated storage and transportation have the potential to enable decentralized biomanufacturing. However, increased thermostability and decreased reaction cost are necessary for further technology adoption. Here, we identify maltodextrin as an additive to cell-free reactions that can act as both a lyoprotectant to increase thermostability and a low-cost energy substrate. As a model, we apply optimized formulations to produce conjugate vaccines for ∼$0.50 per dose after storage at room temperature (∼22 °C) or 37 °C for up to 4 weeks, and ∼$1.00 per dose after storage at 50 °C for up to 4 weeks, with costs based on raw materials purchased at the laboratory scale. We show that these conjugate vaccines generate bactericidal antibodies against enterotoxigenic Escherichia coli (ETEC) O78 O-polysaccharide, a pathogen responsible for diarrheal disease, in immunized mice. We anticipate that our low-cost, thermostable cell-free glycoprotein synthesis system will enable new models of medicine biosynthesis and distribution that bypass cold-chain requirements.
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Affiliation(s)
- Katherine
F. Warfel
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208, United States,Chemistry
of Life Processes Institute, Northwestern
University, 2170 Campus
Drive, Evanston, Illinois 60208, United States,Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological
Institute E136, Evanston, Illinois 60208, United States
| | - Asher Williams
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853 United States
| | - Derek A. Wong
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208, United States,Chemistry
of Life Processes Institute, Northwestern
University, 2170 Campus
Drive, Evanston, Illinois 60208, United States,Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological
Institute E136, Evanston, Illinois 60208, United States
| | - Sarah E. Sobol
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208, United States,Chemistry
of Life Processes Institute, Northwestern
University, 2170 Campus
Drive, Evanston, Illinois 60208, United States,Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological
Institute E136, Evanston, Illinois 60208, United States
| | - Primit Desai
- Biochemistry,
Molecular & Cell Biology, Cornell University, Ithaca, New York 14853 United States
| | - Jie Li
- Department
of Population Medicine and Diagnostic Sciences, College of Veterinary
Medicine, Cornell University, Ithaca, New York 14853, United States
| | - Yung-Fu Chang
- Department
of Population Medicine and Diagnostic Sciences, College of Veterinary
Medicine, Cornell University, Ithaca, New York 14853, United States
| | - Matthew P. DeLisa
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853 United States,Biochemistry,
Molecular & Cell Biology, Cornell University, Ithaca, New York 14853 United States,Cornell
Institute of Biotechnology, Cornell University, Ithaca, New York 14853 United States
| | - Ashty S. Karim
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208, United States,Chemistry
of Life Processes Institute, Northwestern
University, 2170 Campus
Drive, Evanston, Illinois 60208, United States,Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological
Institute E136, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208, United States,Chemistry
of Life Processes Institute, Northwestern
University, 2170 Campus
Drive, Evanston, Illinois 60208, United States,Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological
Institute E136, Evanston, Illinois 60208, United States,Robert
H. Lurie Comprehensive Cancer Center, Northwestern
University, 676 North
Saint Clair Street, Suite 1200, Chicago, Illinois 60611, United States,Simpson
Querrey Institute, Northwestern University, 303 East Superior Street, Suite
11-131, Chicago, Illinois 60611, United States,. Phone: 1-847-497-5007
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12
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Hooe SL, Ellis GA, Medintz IL. Alternative design strategies to help build the enzymatic retrosynthesis toolbox. RSC Chem Biol 2022; 3:1301-1313. [PMID: 36349225 PMCID: PMC9627731 DOI: 10.1039/d2cb00096b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/11/2022] [Indexed: 05/30/2024] Open
Abstract
Most of the complex molecules found in nature still cannot be synthesized by current organic chemistry methods. Given the number of enzymes that exist in nature and the incredible potential of directed evolution, the field of synthetic biology contains perhaps all the necessary building blocks to bring about the realization of applied enzymatic retrosynthesis. Current thinking anticipates that enzymatic retrosynthesis will be implemented using conventional cell-based synthetic biology approaches where requisite native, heterologous, designer, and evolved enzymes making up a given multi-enzyme pathway are hosted by chassis organisms to carry out designer synthesis. In this perspective, we suggest that such an effort should not be limited by solely exploiting living cells and enzyme evolution and describe some useful yet less intensive complementary approaches that may prove especially productive in this grand scheme. By decoupling reactions from the environment of a living cell, a significantly larger portion of potential synthetic chemical space becomes available for exploration; most of this area is currently unavailable to cell-based approaches due to toxicity issues. In contrast, in a cell-free reaction a variety of classical enzymatic approaches can be exploited to improve performance and explore and understand a given enzyme's substrate specificity and catalytic profile towards non-natural substrates. We expect these studies will reveal unique enzymatic capabilities that are not accessible in living cells.
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Affiliation(s)
- Shelby L Hooe
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory Washington DC 20375 USA
- National Research Council Washington DC 20001 USA
| | - Gregory A Ellis
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory Washington DC 20375 USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory Washington DC 20375 USA
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13
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Orsi E, Claassens NJ, Nikel PI, Lindner SN. Optimizing microbial networks through metabolic bypasses. Biotechnol Adv 2022; 60:108035. [PMID: 36096403 DOI: 10.1016/j.biotechadv.2022.108035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 01/29/2023]
Abstract
Metabolism has long been considered as a relatively stiff set of biochemical reactions. This somewhat outdated and dogmatic view has been challenged over the last years, as multiple studies exposed unprecedented plasticity of metabolism by exploring rational and evolutionary modifications within the metabolic network of cell factories. Of particular importance is the emergence of metabolic bypasses, which consist of enzymatic reaction(s) that support unnatural connections between metabolic nodes. Such novel topologies can be generated through the introduction of heterologous enzymes or by upregulating native enzymes (sometimes relying on promiscuous activities thereof). Altogether, the adoption of bypasses resulted in an expansion in the capacity of the host's metabolic network, which can be harnessed for bioproduction. In this review, we discuss modifications to the canonical architecture of central carbon metabolism derived from such bypasses towards six optimization purposes: stoichiometric gain, overcoming kinetic limitations, solving thermodynamic barriers, circumventing toxic intermediates, uncoupling product synthesis from biomass formation, and altering redox cofactor specificity. The metabolic costs associated with bypass-implementation are likewise discussed, including tailoring their design towards improving bioproduction.
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Affiliation(s)
- Enrico Orsi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Biochemistry, Charité Universitätsmedizin, Virchowweg 6, 10117 Berlin, Germany.
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14
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King E, Cui Y, Aspacio D, Nicklen F, Zhang L, Maxel S, Luo R, Siegel JB, Aitchison E, Li H. Engineering Embden-Meyerhof-Parnas Glycolysis to Generate Noncanonical Reducing Power. ACS Catal 2022; 12:8582-8592. [PMID: 37622090 PMCID: PMC10449333 DOI: 10.1021/acscatal.2c01837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noncanonical cofactors such as nicotinamide mononucleotide (NMN+) supplant the electron-transfer functionality of the natural cofactors, NAD(P)+, at a lower cost in cell-free biomanufacturing and enable orthogonal electron delivery in whole-cell metabolic engineering. Here, we redesign the high-flux Embden-Meyerhof-Parnas (EMP) glycolytic pathway to generate NMN+-based reducing power, by engineering Streptococcus mutans glyceraldehyde-3-phosphate dehydrogenase (Sm GapN) to utilize NMN+. Through iterative rounds of rational design, we discover the variant GapN Penta (P179K-F153S-S330R-I234E-G210Q) with high NMN+-dependent activity and GapN Ortho (P179K-F153S-S330R-I234E-G214E) with ~3.4 × 106-fold switch in cofactor specificity from its native cofactor NADP+ to NMN+. GapN Ortho is further demonstrated to function in Escherichia coli only in the presence of NMN+, enabling orthogonal control of glucose utilization. Molecular dynamics simulation and residue network connectivity analysis indicate that mutations altering cofactor specificity must be coordinated to maintain the appropriate degree of backbone flexibility to position the catalytic cysteine. These results provide a strategy to guide future designs of NMN+-dependent enzymes and establish the initial steps toward an orthogonal EMP pathway with biomanufacturing potential.
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Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Youtian Cui
- Genome Center, University of California, Davis, Davis, California 95616, United States
| | - Derek Aspacio
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Frances Nicklen
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Linyue Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Sarah Maxel
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Department of Chemical and Biomolecular Engineering, and Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Justin B Siegel
- Department of Chemistry, Genome Center, and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
| | - Erick Aitchison
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering and Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
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15
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Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria. Nat Commun 2022; 13:3058. [PMID: 35650184 PMCID: PMC9160091 DOI: 10.1038/s41467-022-30571-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/09/2022] [Indexed: 11/12/2022] Open
Abstract
Carbon-negative synthesis of biochemical products has the potential to mitigate global CO2 emissions. An attractive route to do this is the reverse β-oxidation (r-BOX) pathway coupled to the Wood-Ljungdahl pathway. Here, we optimize and implement r-BOX for the synthesis of C4-C6 acids and alcohols. With a high-throughput in vitro prototyping workflow, we screen 762 unique pathway combinations using cell-free extracts tailored for r-BOX to identify enzyme sets for enhanced product selectivity. Implementation of these pathways into Escherichia coli generates designer strains for the selective production of butanoic acid (4.9 ± 0.1 gL−1), as well as hexanoic acid (3.06 ± 0.03 gL−1) and 1-hexanol (1.0 ± 0.1 gL−1) at the best performance reported to date in this bacterium. We also generate Clostridium autoethanogenum strains able to produce 1-hexanol from syngas, achieving a titer of 0.26 gL−1 in a 1.5 L continuous fermentation. Our strategy enables optimization of r-BOX derived products for biomanufacturing and industrial biotechnology. An attractive route for carbon-negative synthesis of biochemical products is the reverse β-oxidation pathway coupled to the Wood-Ljungdahl pathway. Here the authors use a high-throughput in vitro prototyping workflow to screen 762 unique pathway combinations using cell-free extracts tailored for r-BOX to identify enzyme sets for enhanced product selectivity.
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16
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GAN R, Cabezas MD, Pan M, Zhang H, Hu G, Clark LG, Jewett MC, Nicol R. High-Throughput Regulatory Part Prototyping and Analysis by Cell-Free Protein Synthesis and Droplet Microfluidics. ACS Synth Biol 2022; 11:2108-2120. [PMID: 35549070 DOI: 10.1021/acssynbio.2c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Engineering regulatory parts for improved performance in genetic programs has played a pivotal role in the development of the synthetic biology cell programming toolbox. Here, we report the development of a novel high-throughput platform for regulatory part prototyping and analysis that leverages the advantages of engineered DNA libraries, cell-free protein synthesis (CFPS), high-throughput emulsion droplet microfluidics, standard flow sorting adapted to screen droplet reactions, and next-generation sequencing (NGS). With this integrated platform, we screened the activity of millions of genetic parts within hours, followed by NGS retrieval of the improved designs. This in vitro platform is particularly valuable for engineering regulatory parts of nonmodel organisms, where in vivo high-throughput screening methods are not readily available. The platform can be extended to multipart screening of complete genetic programs to optimize yield and stability.
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Affiliation(s)
- Rui GAN
- Broad Institute of MIT and Harvard, Cambridge, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Maria D. Cabezas
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3120, United States
| | - Ming Pan
- Broad Institute of MIT and Harvard, Cambridge, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Huaibin Zhang
- Broad Institute of MIT and Harvard, Cambridge, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Gang Hu
- Broad Institute of MIT and Harvard, Cambridge, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Lauren G. Clark
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3120, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3120, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3120, United States
- Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3120, United States
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3120, United States
| | - Robert Nicol
- Broad Institute of MIT and Harvard, Cambridge, 415 Main Street, Cambridge, Massachusetts 02142, United States
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17
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Sridharan H, Piorino F, Styczynski MP. Systems biology-based analysis of cell-free systems. Curr Opin Biotechnol 2022; 75:102703. [PMID: 35247659 DOI: 10.1016/j.copbio.2022.102703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/07/2021] [Accepted: 02/03/2022] [Indexed: 11/28/2022]
Abstract
Cell-free expression systems are becoming increasingly widely used due to their diverse applications in biotechnology. Despite this rapid expansion in adoption, many aspects of cell-free systems remain surprisingly poorly understood. Systems biology approaches make it possible to characterize cell-free systems deeply and broadly to better understand their underlying complexity. Here, we review recent systems biology studies that have provided insight into cell-free systems. We focus on characterization of the cell-free proteome, including its dependence on preparation protocol and host strain, as well as the cell-free metabolome and the relationship of endogenous metabolism to system performance. We conclude by highlighting promising future research directions.
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Affiliation(s)
- Harini Sridharan
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332-0100, United States
| | - Fernanda Piorino
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332-0100, United States
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332-0100, United States.
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