1
|
Piorino F, Patterson AT, Han Y, Styczynski MP. Plasmid Crosstalk in Cell-Free Expression Systems. ACS Synth Biol 2023; 12:2843-2856. [PMID: 37756020 PMCID: PMC10594874 DOI: 10.1021/acssynbio.3c00412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Indexed: 09/28/2023]
Abstract
Although cell-free protein expression has been widely used for the synthesis of single proteins, cell-free synthetic biology has rapidly expanded to new, more complex applications. One such application is the prototyping or implementation of complex genetic networks involving the expression of multiple proteins at precise ratios, often from different plasmids. However, expression of multiple proteins from multiple plasmids may inadvertently result in unexpected, off-target changes to the levels of the proteins being expressed, a phenomenon termed plasmid crosstalk. Here, we show that the effects of plasmid crosstalk─even at the qualitative level of increases vs decreases in protein expression─depend on the concentration of plasmids in the reaction and the type of transcriptional machinery involved in the expression. This crosstalk can have a significant impact on genetic circuitry function and even interpretation of simple experimental results and thus should be taken into consideration during the development of cell-free applications.
Collapse
Affiliation(s)
- Fernanda Piorino
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Alexandra T. Patterson
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Yue Han
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Mark P. Styczynski
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| |
Collapse
|
2
|
Martin JP, Rasor BJ, DeBonis J, Karim AS, Jewett MC, Tyo KEJ, Broadbelt LJ. A dynamic kinetic model captures cell-free metabolism for improved butanol production. Metab Eng 2023; 76:133-145. [PMID: 36724840 DOI: 10.1016/j.ymben.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/30/2022] [Accepted: 01/25/2023] [Indexed: 01/30/2023]
Abstract
Cell-free systems are useful tools for prototyping metabolic pathways and optimizing the production of various bioproducts. Mechanistically-based kinetic models are uniquely suited to analyze dynamic experimental data collected from cell-free systems and provide vital qualitative insight. However, to date, dynamic kinetic models have not been applied with rigorous biological constraints or trained on adequate experimental data to the degree that they would give high confidence in predictions and broadly demonstrate the potential for widespread use of such kinetic models. In this work, we construct a large-scale dynamic model of cell-free metabolism with the goal of understanding and optimizing butanol production in a cell-free system. Using a combination of parameterization methods, the resultant model captures experimental metabolite measurements across two experimental conditions for nine metabolites at timepoints between 0 and 24 h. We present analysis of the model predictions, provide recommendations for butanol optimization, and identify the aldehyde/alcohol dehydrogenase as the primary bottleneck in butanol production. Sensitivity analysis further reveals the extent to which various parameters are constrained, and our approach for probing valid parameter ranges can be applied to other modeling efforts.
Collapse
Affiliation(s)
- Jacob P Martin
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
| | - Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
| | - Jonathon DeBonis
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.
| |
Collapse
|
3
|
Romantseva EF, Tack DS, Alperovich N, Ross D, Strychalski EA. Best Practices for DNA Template Preparation Toward Improved Reproducibility in Cell-Free Protein Production. Methods Mol Biol 2022; 2433:3-50. [PMID: 34985735 DOI: 10.1007/978-1-0716-1998-8_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Performance variability is a common challenge in cell-free protein production and hinders a wider adoption of these systems for both research and biomanufacturing. While the inherent stochasticity and complexity of biology likely contributes to variability, other systematic factors may also play a role, including the source and preparation of the cell extract, the composition of the supplemental reaction buffer, the facility at which experiments are conducted, and the human operator (Cole et al. ACS Synth Biol 8:2080-2091, 2019). Variability in protein production could also arise from differences in the DNA template-specifically the amount of functional DNA added to a cell-free reaction and the quality of the DNA preparation in terms of contaminants and strand breakage. Here, we present protocols and suggest best practices optimized for DNA template preparation and quantitation for cell-free systems toward reducing variability in cell-free protein production.
Collapse
Affiliation(s)
| | - Drew S Tack
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nina Alperovich
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | |
Collapse
|
4
|
Wu K, Green AA. Detection of Norovirus Using Paper-Based Cell-Free Systems. Methods Mol Biol 2022; 2433:375-390. [PMID: 34985757 DOI: 10.1007/978-1-0716-1998-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Norovirus infections are the leading cause of foodborne illness and human gastroenteritis, afflicting hundreds of millions of people each year. Molecular assays with the capacity to detect norovirus without expensive equipment and with high sensitivity and specificity represent useful tools to track and contain future outbreaks. Here we describe how norovirus can be detected in low-cost paper-based cell-free reactions. These assays combine freeze-dried, thermostable cell-free transcription-translation reactions with toehold switch riboregulators designed to target the norovirus genome, enabling convenient colorimetric assay readouts. Coupling cell-free reactions with synbody-based viral enrichment and isothermal amplification enables detection of norovirus from clinical samples down to concentrations as low as 270 zM. These diagnostic tests are promising assays for confronting norovirus outbreaks and can be adapted to a variety of other human pathogens.
Collapse
Affiliation(s)
- Kaiyue Wu
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology and Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
| | - Alexander A Green
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
| |
Collapse
|
5
|
Cole SD, Miklos AE, Chiao AC, Sun ZZ, Lux MW. Methodologies for preparation of prokaryotic extracts for cell-free expression systems. Synth Syst Biotechnol 2020; 5:252-267. [PMID: 32775710 PMCID: PMC7398980 DOI: 10.1016/j.synbio.2020.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022] Open
Abstract
Cell-free systems that mimic essential cell functions, such as gene expression, have dramatically expanded in recent years, both in terms of applications and widespread adoption. Here we provide a review of cell-extract methods, with a specific focus on prokaryotic systems. Firstly, we describe the diversity of Escherichia coli genetic strains available and their corresponding utility. We then trace the history of cell-extract methodology over the past 20 years, showing key improvements that lower the entry level for new researchers. Next, we survey the rise of new prokaryotic cell-free systems, with associated methods, and the opportunities provided. Finally, we use this historical perspective to comment on the role of methodology improvements and highlight where further improvements may be possible.
Collapse
Affiliation(s)
- Stephanie D. Cole
- US Army Combat Capabilities Development Command Chemical Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| | - Aleksandr E. Miklos
- US Army Combat Capabilities Development Command Chemical Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| | - Abel C. Chiao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Synvitrobio Inc., San Francisco, CA, USA
| | - Zachary Z. Sun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Synvitrobio Inc., San Francisco, CA, USA
| | - Matthew W. Lux
- US Army Combat Capabilities Development Command Chemical Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| |
Collapse
|
6
|
Lee MS, Hung CS, Phillips DA, Buck CC, Gupta MK, Lux MW. Silk fibroin as an additive for cell-free protein synthesis. Synth Syst Biotechnol 2020; 5:145-154. [PMID: 32637668 PMCID: PMC7320238 DOI: 10.1016/j.synbio.2020.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 01/06/2023] Open
Abstract
Cell-free systems contain many proteins and metabolites required for complex functions such as transcription and translation or multi-step metabolic conversions. Research into expanding the delivery of these systems by drying or by embedding into other materials is enabling new applications in sensing, point-of-need manufacturing, and responsive materials. Meanwhile, silk fibroin from the silk worm, Bombyx mori, has received attention as a protective additive for dried enzyme formulations and as a material to build biocompatible hydrogels for controlled localization or delivery of biomolecular cargoes. In this work, we explore the effects of silk fibroin as an additive in cell-free protein synthesis (CFPS) reactions. Impacts of silk fibroin on CFPS activity and stability after drying, as well as the potential for incorporation of CFPS into hydrogels of crosslinked silk fibroin are assessed. We find that simple addition of silk fibroin increased productivity of the CFPS reactions by up to 42%, which we attribute to macromolecular crowding effects. However, we did not find evidence that silk fibroin provides a protective effects after drying as previously described for purified enzymes. Further, the enzymatic crosslinking transformations of silk fibroin typically used to form hydrogels are inhibited in the presence of the CFPS reaction mixture. Crosslinking attempts did not impact CFPS activity, but did yield localized protein aggregates rather than a hydrogel. We discuss the mechanisms at play in these results and how the silk fibroin-CFPS system might be improved for the design of cell-free devices.
Collapse
Affiliation(s)
- Marilyn S. Lee
- US Army Combat Capabilities Development Command Chemical and Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| | - Chia-Suei Hung
- US Air Force Research Laboratory, 2179 12th St., B652/R122 Wright-Patterson Air Force Base, OH, 45433, USA
| | - Daniel A. Phillips
- US Naval Research Laboratory Center for Bio/Molecular Science and Engineering, Bldg. 42, Room 303 4555 Overlook Ave. Washington, DC 20375, UES Inc., 4401 Dayton Xenia Rd., Beavercreek, OH 45432, USA
| | - Chelsea C. Buck
- US Air Force Research Laboratory, 2179 12th St., B652/R122 Wright-Patterson Air Force Base, OH, 45433, USA
- US Naval Research Laboratory Center for Bio/Molecular Science and Engineering, Bldg. 42, Room 303 4555 Overlook Ave. Washington, DC 20375, UES Inc., 4401 Dayton Xenia Rd., Beavercreek, OH 45432, USA
| | - Maneesh K. Gupta
- US Air Force Research Laboratory, 2179 12th St., B652/R122 Wright-Patterson Air Force Base, OH, 45433, USA
| | - Matthew W. Lux
- US Army Combat Capabilities Development Command Chemical and Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| |
Collapse
|
7
|
Zhuang L, Huang S, Liu WQ, Karim AS, Jewett MC, Li J. Total in vitro biosynthesis of the nonribosomal macrolactone peptide valinomycin. Metab Eng 2020; 60:37-44. [PMID: 32224263 DOI: 10.1016/j.ymben.2020.03.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/20/2020] [Accepted: 03/22/2020] [Indexed: 11/16/2022]
Abstract
Natural products are important because of their significant pharmaceutical properties such as antiviral, antimicrobial, and anticancer activity. Recent breakthroughs in DNA sequencing reveal that a great number of cryptic natural product biosynthetic gene clusters are encoded in microbial genomes, for example, those of Streptomyces species. However, it is still challenging to access compounds from these clusters because many source organisms are uncultivable or the genes are silent during laboratory cultivation. To address this challenge, we develop an efficient cell-free platform for the rapid, in vitro total biosynthesis of the nonribosomal peptide valinomycin as a model. We achieve this goal in two ways. First, we used a cell-free protein synthesis (CFPS) system to express the entire valinomycin biosynthetic gene cluster (>19 kb) in a single-pot reaction, giving rise to approximately 37 μg/L of valinomycin after optimization. Second, we coupled CFPS with cell-free metabolic engineering system by mixing two enzyme-enriched cell lysates to perform a two-stage biosynthesis. This strategy improved valinomycin production ~5000-fold to nearly 30 mg/L. We expect that cell-free biosynthetic systems will provide a new avenue to express, discover, and characterize natural product gene clusters of interest in vitro.
Collapse
Affiliation(s)
- Lei Zhuang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Shuhui Huang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, United States.
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| |
Collapse
|
8
|
Mahour R, Klapproth J, Rexer TFT, Schildbach A, Klamt S, Pietzsch M, Rapp E, Reichl U. Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine. J Biotechnol 2018; 283:120-129. [PMID: 30044949 DOI: 10.1016/j.jbiotec.2018.07.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/17/2018] [Accepted: 07/21/2018] [Indexed: 12/17/2022]
Abstract
In spite of huge endeavors in cell line engineering to produce glycoproteins with desired and uniform glycoforms, it is still not possible in vivo. Alternatively, in vitro glycoengineering can be used for the modification of glycans. However, in vitro glycoengineering relies on expensive nucleotide sugars, such as uridine 5'-diphospho-N-acetylglucosamine (UDP-GlcNAc) which serves as GlcNAc donor for the synthesis of various glycans. In this work, we present a systematic study for the cell-free de novo synthesis and regeneration of UDP-GlcNAc from polyphosphate, UMP and GlcNAc by a cascade of five enzymes (N-acetylhexosamine kinase (NahK), Glc-1P uridyltransferase (GalU), uridine monophosphate kinase (URA6), polyphosphate kinase (PPK3), and inorganic diphosphatase (PmPpA). All enzymes were expressed in E. coli BL21 Gold (DE3) and purified using immobilized metal affinity chromatography (IMAC). Results from one-pot experiments demonstrate the successful production of UDP-GlcNAc with a yield approaching 100%. The highest volumetric productivity of the cascade was about 0.81 g L-1 h-1 of UDP-GlcNAc. A simple model based on mass action kinetics was sufficient to capture the dynamic behavior of the multienzyme pathway. Moreover, a design equation based on metabolic control analysis was established to investigate the effect of enzyme concentration on the UDP-GlcNAc flux and to demonstrate that the flux of UDP-GlcNAc can be controlled by means of the enzyme concentrations. The effect of temperature on the UDP-GlcNAc flux followed an Arrhenius equation and the optimal co-factor concentration (Mg2+) for high UDP-GlcNAc synthesis rates depended on the working temperature. In conclusion, the study covers the entire engineering process of a multienzyme cascade, i.e. pathway design, enzyme expression, enzyme purification, reaction kinetics and investigation of the influence of basic parameters (temperature, co-factor concentration, enzyme concentration) on the synthesis rate. Thus, the study lays the foundation for future cascade optimization, preparative scale UDP-GlcNAc synthesis and for in situ coupling of the network with UDP-GlcNAc transferases to efficiently regenerate UDP-GlcNAc. Hence, this study provides a further step towards cost-effective in vitro glycoengineering of antibodies and other glycosylated proteins.
Collapse
Affiliation(s)
- Reza Mahour
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Jan Klapproth
- Martin Luther University Halle-Wittenberg, Institute of Pharmacy, Department of Downstream Processing, Halle (Saale), Germany.
| | - Thomas F T Rexer
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Anna Schildbach
- Martin Luther University Halle-Wittenberg, Institute of Pharmacy, Department of Downstream Processing, Halle (Saale), Germany.
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Analysis and Redesign of Biological Networks, Magdeburg, Germany.
| | - Markus Pietzsch
- Martin Luther University Halle-Wittenberg, Institute of Pharmacy, Department of Downstream Processing, Halle (Saale), Germany.
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany; Otto-von-Guericke University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany.
| |
Collapse
|
9
|
Satagopan S, Sun Y, Parquette JR, Tabita FR. Synthetic CO 2-fixation enzyme cascades immobilized on self-assembled nanostructures that enhance CO 2/O 2 selectivity of RubisCO. Biotechnol Biofuels 2017; 10:175. [PMID: 28694846 PMCID: PMC5501267 DOI: 10.1186/s13068-017-0861-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND With increasing concerns over global warming and depletion of fossil-fuel reserves, it is attractive to develop innovative strategies to assimilate CO2, a greenhouse gas, into usable organic carbon. Cell-free systems can be designed to operate as catalytic platforms with enzymes that offer exceptional selectivity and efficiency, without the need to support ancillary reactions of metabolic pathways operating in intact cells. Such systems are yet to be exploited for applications involving CO2 utilization and subsequent conversion to valuable products, including biofuels. The Calvin-Benson-Bassham (CBB) cycle and the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) play a pivotal role in global CO2 fixation. RESULTS We hereby demonstrate the co-assembly of two RubisCO-associated multienzyme cascades with self-assembled synthetic amphiphilic peptide nanostructures. The immobilized enzyme cascades sequentially convert either ribose-5-phosphate (R-5-P) or glucose, a simpler substrate, to ribulose 1,5-bisphosphate (RuBP), the acceptor for incoming CO2 in the carboxylation reaction catalyzed by RubisCO. Protection from proteolytic degradation was observed in nanostructures associated with the small dimeric form of RubisCO and ancillary enzymes. Furthermore, nanostructures associated with a larger variant of RubisCO resulted in a significant enhancement of the enzyme's selectivity towards CO2, without adversely affecting the catalytic activity. CONCLUSIONS The ability to assemble a cascade of enzymes for CO2 capture using self-assembling nanostructure scaffolds with functional enhancements show promise for potentially engineering entire pathways (with RubisCO or other CO2-fixing enzymes) to redirect carbon from industrial effluents into useful bioproducts.
Collapse
Affiliation(s)
- Sriram Satagopan
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210-1292 USA
| | - Yuan Sun
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210-1185 USA
| | - Jon R. Parquette
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210-1185 USA
| | - F. Robert Tabita
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210-1292 USA
| |
Collapse
|
10
|
Semenchenko A, Oliveira G, Atman AP. Hybrid agent-based model for quantitative in-silico cell-free protein synthesis. Biosystems 2016; 150:22-34. [PMID: 27501921 DOI: 10.1016/j.biosystems.2016.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 07/05/2016] [Accepted: 07/17/2016] [Indexed: 12/15/2022]
Abstract
An advanced vision of the mRNA translation is presented through a hybrid modeling approach. The dynamics of the polysome formation was investigated by computer simulation that combined agent-based model and fine-grained Markov chain representation of the chemical kinetics. This approach allowed for the investigation of the polysome dynamics under non-steady-state and non-continuum conditions. The model is validated by the quantitative comparison of the simulation results and Luciferase protein production in cell-free system, as well as by testing of the hypothesis regarding the two possible mechanisms of the Edeine antibiotic. Calculation of the Hurst exponent demonstrated a relationship between the microscopic properties of amino acid elongation and the fractal dimension of the translation duration time series. The temporal properties of the amino acid elongation have indicated an anti-persistent behavior under low mRNA occupancy and evinced the appearance of long range interactions within the mRNA-ribosome system for high ribosome density. The dynamic and temporal characteristics of the polysomal system presented here can have a direct impact on the studies of the co-translation protein folding and provide a validated platform for cell-free system studies.
Collapse
|