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Darvishi F, Rafatiyan S, Abbaspour Motlagh Moghaddam MH, Atkinson E, Ledesma-Amaro R. Applications of synthetic yeast consortia for the production of native and non-native chemicals. Crit Rev Biotechnol 2024; 44:15-30. [PMID: 36130800 DOI: 10.1080/07388551.2022.2118569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/03/2022] [Accepted: 08/19/2022] [Indexed: 11/03/2022]
Abstract
The application of microbial consortia is a new approach in synthetic biology. Synthetic yeast consortia, simple or complex synthetic mixed cultures, have been used for the production of various metabolites. Cooperation between the members of a consortium and cross-feeding can be applied to create stable microbial communication. These consortia can: consume a variety of substrates, perform more complex functions, produce metabolites in high titer, rate, and yield (TRY), and show higher stability during industrial fermentations. Due to the new research context of synthetic consortia, few yeasts were used to build these consortia, including Saccharomyces cerevisiae, Pichia pastoris, and Yarrowia lipolytica. Here, application of the yeasts for design of synthetic microbial consortia and their advantages and bottlenecks for effective and robust production of valuable metabolites from bioresource, including: cellulose, xylose, glycerol and so on, have been reviewed. Key trends and challenges are also discussed for the future development of synthetic yeast consortia.
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Affiliation(s)
- Farshad Darvishi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
- Research Center for Applied Microbiology and Microbial Biotechnology (CAMB), Alzahra University, Tehran, Iran
| | - Sajad Rafatiyan
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | | | - Eliza Atkinson
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
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2
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Besada-Lombana PB, Chen W, Da Silva NA. An extracellular glucose sensor for substrate-dependent secretion and display of cellulose-degrading enzymes. Biotechnol Bioeng 2024; 121:403-408. [PMID: 37749915 DOI: 10.1002/bit.28549] [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: 06/27/2023] [Revised: 08/17/2023] [Accepted: 08/30/2023] [Indexed: 09/27/2023]
Abstract
The efficient hydrolysis of lignocellulosic biomass into fermentable sugars is key for viable economic production of biofuels and biorenewable chemicals from second-generation feedstocks. Consolidated bioprocessing (CBP) combines lignocellulose saccharification and chemical production in a single step. To avoid wasting valuable resources during CBP, the selective secretion of enzymes (independent or attached to the surface) based on the carbon source available is advantageous. To enable enzyme expression and secretion based on extracellular glucose levels, we implemented a G-protein-coupled receptor (GPCR)-based extracellular glucose sensor; this allows the secretion and display of cellulases in the presence of the cellulosic fraction of lignocellulose by leveraging cellobiose-dependent signal amplification. We focused on the glucose-responsiveness of the HXT1 promoter and engineered PHXT1 by changing its core to that of the strong promoter PTHD3 , increasing extracellular enzyme activity by 81%. We then demonstrated glucose-mediated expression and cell-surface display of the β-glucosidase BglI on the surface of Saccharomyces cerevisiae. The display system was further optimized by re-directing fatty acid pools from lipid droplet synthesis toward formation of membrane precursors via knock-out of PAH1. This resulted in an up to 4.2-fold improvement with respect to the baseline strain. Finally, we observed cellobiose-dependent signal amplification of the system with an increase in enzymatic activity of up to 3.1-fold when cellobiose was added.
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Affiliation(s)
- Pamela B Besada-Lombana
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Nancy A Da Silva
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California, USA
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3
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Lamote B, da Fonseca MJM, Vanderstraeten J, Meert K, Elias M, Briers Y. Current challenges in designer cellulosome engineering. Appl Microbiol Biotechnol 2023; 107:2755-2770. [PMID: 36941434 DOI: 10.1007/s00253-023-12474-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/23/2023]
Abstract
Designer cellulosomes (DCs) are engineered multi-enzyme complexes, comprising carbohydrate-active enzymes attached to a common backbone, the scaffoldin, via high-affinity cohesin-dockerin interactions. The use of DCs in the degradation of renewable biomass polymers is a promising approach for biorefineries. Indeed, DCs have shown significant hydrolytic activities due to the enhanced enzyme-substrate proximity and inter-enzyme synergies, but technical hurdles in DC engineering have hindered further progress towards industrial application. The challenge in DC engineering lies in the large diversity of possible building blocks and architectures, resulting in a multivariate and immense design space. Simultaneously, the precise DC composition affects many relevant parameters such as activity, stability, and manufacturability. Since protein engineers face a lack of high-throughput approaches to explore this vast design space, DC engineering may result in an unsatisfying outcome. This review provides a roadmap to guide researchers through the process of DC engineering. Each step, starting from concept to evaluation, is described and provided with its challenges, along with possible solutions, both for DCs that are assembled in vitro or are displayed on the yeast cell surface. KEY POINTS: • Construction of designer cellulosomes is a multi-step process. • Designer cellulosome research deals with multivariate construction challenges. • Boosting designer cellulosome efficiency requires exploring a vast design space.
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Affiliation(s)
- Babette Lamote
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | | | - Julie Vanderstraeten
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Kenan Meert
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Marte Elias
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium.
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4
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Zhang C, Chen H, Zhu Y, Zhang Y, Li X, Wang F. Saccharomyces cerevisiae cell surface display technology: Strategies for improvement and applications. Front Bioeng Biotechnol 2022; 10:1056804. [PMID: 36568309 PMCID: PMC9767963 DOI: 10.3389/fbioe.2022.1056804] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Microbial cell surface display technology provides a powerful platform for engineering proteins/peptides with enhanced properties. Compared to the classical intracellular and extracellular expression (secretion) systems, this technology avoids enzyme purification, substrate transport processes, and is an effective solution to enzyme instability. Saccharomyces cerevisiae is well suited to cell surface display as a common cell factory for the production of various fuels and chemicals, with the advantages of large cell size, being a Generally Regarded As Safe (GRAS) organism, and post-translational processing of secreted proteins. In this review, we describe various strategies for constructing modified S. cerevisiae using cell surface display technology and outline various applications of this technology in industrial processes, such as biofuels and chemical products, environmental pollution treatment, and immunization processes. The approaches for enhancing the efficiency of cell surface display are also discussed.
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Affiliation(s)
- Chenmeng Zhang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Hongyu Chen
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Yiping Zhu
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Yu Zhang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Xun Li
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Fei Wang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China,*Correspondence: Fei Wang,
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5
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Tsai SL, Sun Q, Chen W. Advances in consolidated bioprocessing using synthetic cellulosomes. Curr Opin Biotechnol 2022; 78:102840. [PMID: 36356377 DOI: 10.1016/j.copbio.2022.102840] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/02/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022]
Abstract
The primary obstacle impeding the more widespread use of biomass for energy and chemical production is the absence of a low-cost technology for overcoming their recalcitrant nature. It has been shown that the overall cost can be reduced by using a 'consolidated' bioprocessing (CBP) approach, in which enzyme production, biomass hydrolysis, and sugar fermentation can be combined. Cellulosomes are enzyme complexes found in many anaerobic microorganisms that are highly efficient for biomass depolymerization. While initial efforts to display synthetic cellulosomes have been successful, the overall conversion is still low for practical use. This limitation has been partially alleviated by displaying more complex cellulsome structures either via adaptive assembly or by using synthetic consortia. Since synthetic cellulosome nanostructures have also been created using either protein nanoparticles or DNA as a scaffold, there is the potential to tether these nanostructures onto living cells in order to further enhance the overall efficiency.
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Affiliation(s)
- Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei City 106335, Taiwan
| | - Qing Sun
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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6
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Atkinson E, Tuza Z, Perrino G, Stan GB, Ledesma-Amaro R. Resource-aware whole-cell model of division of labour in a microbial consortium for complex-substrate degradation. Microb Cell Fact 2022; 21:115. [PMID: 35698129 PMCID: PMC9195437 DOI: 10.1186/s12934-022-01842-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Low-cost sustainable feedstocks are essential for commercially viable biotechnologies. These feedstocks, often derived from plant or food waste, contain a multitude of different complex biomolecules which require multiple enzymes to hydrolyse and metabolise. Current standard biotechnology uses monocultures in which a single host expresses all the proteins required for the consolidated bioprocess. However, these hosts have limited capacity for expressing proteins before growth is impacted. This limitation may be overcome by utilising division of labour (DOL) in a consortium, where each member expresses a single protein of a longer degradation pathway. RESULTS Here, we model a two-strain consortium, with one strain expressing an endohydrolase and a second strain expressing an exohydrolase, for cooperative degradation of a complex substrate. Our results suggest that there is a balance between increasing expression to enhance degradation versus the burden that higher expression causes. Once a threshold of burden is reached, the consortium will consistently perform better than an equivalent single-cell monoculture. CONCLUSIONS We demonstrate that resource-aware whole-cell models can be used to predict the benefits and limitations of using consortia systems to overcome burden. Our model predicts the region of expression where DOL would be beneficial for growth on starch, which will assist in making informed design choices for this, and other, complex-substrate degradation pathways.
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Affiliation(s)
- Eliza Atkinson
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Zoltan Tuza
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Giansimone Perrino
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK
| | - Guy-Bart Stan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK.
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW72AZ, UK.
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Sharma J, Kumar V, Prasad R, Gaur NA. Engineering of Saccharomyces cerevisiae as a consolidated bioprocessing host to produce cellulosic ethanol: Recent advancements and current challenges. Biotechnol Adv 2022; 56:107925. [DOI: 10.1016/j.biotechadv.2022.107925] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/24/2022] [Accepted: 02/06/2022] [Indexed: 01/01/2023]
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8
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Sun Q, Raeeszadeh-Sarmazdeh M, Tsai SL, Chen W. Strategies for Multienzyme Assemblies. Methods Mol Biol 2022; 2487:113-131. [PMID: 35687232 DOI: 10.1007/978-1-0716-2269-8_7] [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: 06/15/2023]
Abstract
Proteins are not designed to be standalone entities and must coordinate their collective action for optimum performance. Nature has developed through evolution the ability to co-localize the functional partners of a cascade enzymatic reaction in order to ensure efficient exchange of intermediates. Inspired by these natural designs, synthetic scaffolds have been created to enhance the overall biological pathway performance. In this chapter, we describe several DNA- and protein-based scaffold approaches to assemble artificial enzyme cascades for a wide range of applications. We highlight the key benefits and drawbacks of these approaches to provide insights on how to choose the appropriate scaffold for different cascade systems.
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Affiliation(s)
- Qing Sun
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | | | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei City, Taiwan
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
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9
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Ding Q, Liu Y, Hu G, Guo L, Gao C, Chen X, Chen W, Chen J, Liu L. Engineering Escherichia coli biofilm to increase contact surface for shikimate and L-malate production. BIORESOUR BIOPROCESS 2021; 8:118. [PMID: 38650289 PMCID: PMC10992329 DOI: 10.1186/s40643-021-00470-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/22/2021] [Indexed: 11/10/2022] Open
Abstract
Microbial organelles are a promising model to promote cellular functions for the production of high-value chemicals. However, the concentrations of enzymes and nanoparticles are limited by the contact surface in single Escherichia coli cells. Herein, the definition of contact surface is to improve the amylase and CdS nanoparticles concentration for enhancing the substrate starch and cofactor NADH utilization. In this study, two biofilm-based strategies were developed to improve the contact surface for the production of shikimate and L-malate. First, the contact surface of E. coli was improved by amylase self-assembly with a blue light-inducible biofilm-based SpyTag/SpyCatcher system. This system increased the glucose concentration by 20.7% and the starch-based shikimate titer to 50.96 g L-1, which showed the highest titer with starch as substrate. Then, the contact surface of E. coli was improved using a biofilm-based CdS-biohybrid system by light-driven system, which improved the NADH concentration by 83.3% and increased the NADH-dependent L-malate titer to 45.93 g L-1. Thus, the biofilm-based strategies can regulate cellular functions to increase the efficiency of microbial cell factories based on the optogenetics, light-driven, and metabolic engineering.
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Affiliation(s)
- Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Yadi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Guipeng Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China.
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10
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Pacheco AR, Segrè D. An evolutionary algorithm for designing microbial communities via environmental modification. J R Soc Interface 2021; 18:20210348. [PMID: 34157894 PMCID: PMC8220269 DOI: 10.1098/rsif.2021.0348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Despite a growing understanding of how environmental composition affects microbial communities, it remains difficult to apply this knowledge to the rational design of synthetic multispecies consortia. This is because natural microbial communities can harbour thousands of different organisms and environmental substrates, making up a vast combinatorial space that precludes exhaustive experimental testing and computational prediction. Here, we present a method based on the combination of machine learning and metabolic modelling that selects optimal environmental compositions to produce target community phenotypes. In this framework, dynamic flux balance analysis is used to model the growth of a community in candidate environments. A genetic algorithm is then used to evaluate the behaviour of the community relative to a target phenotype, and subsequently adjust the environment to allow the organisms to approach this target. We apply this iterative process to thousands of in silico communities of varying sizes, showing how it can rapidly identify environments that yield desired taxonomic compositions and patterns of metabolic exchange. Moreover, this combination of approaches produces testable predictions for the assembly of experimental microbial communities with specific properties and can facilitate rational environmental design processes for complex microbiomes.
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Affiliation(s)
- Alan R Pacheco
- Graduate Program in Bioinformatics and Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Daniel Segrè
- Graduate Program in Bioinformatics and Biological Design Center, Boston University, Boston, MA 02215, USA.,Department of Biology, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,Department of Physics, Boston University, Boston, MA 02215, USA
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11
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Kelly EE, Fischer AM, Collins CH. Drawing up a collaborative contract: Amino acid cross-feeding between interspecies bacterial pairs. Biotechnol Bioeng 2021; 118:3138-3149. [PMID: 34027999 DOI: 10.1002/bit.27837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/09/2021] [Accepted: 05/05/2021] [Indexed: 01/04/2023]
Abstract
Synthetic microbial communities have the potential to enable new platforms for bioproduction of biofuels and biopharmaceuticals. However, using engineered communities is often assumed to be difficult because of anticipated challenges in establishing and controlling community composition. Cross-feeding between microbial auxotrophs has the potential to facilitate coculture growth and stability through a mutualistic ecological interaction. We assessed cross-feeding between 13 Escherichia coli amino acid auxotrophs paired with a leucine auxotroph of Bacillus megaterium. We developed a minimal medium capable of supporting the growth of both bacteria and used the media to study coculture growth of the 13 interspecies pairs of auxotrophs in batch and continuous culture, as well as on semi-solid media. In batch culture, 8 of 13 pairs of auxotrophs were observed to grow in coculture. We developed a new metric to quantify the impact of cross-feeding on coculture growth. Six pairs also showed long-term stability in continuous culture, where coculture growth at different dilution rates highlighted differences in cross-feeding amongst the pairs. Finally, we found that cross-feeding-dependent growth on semi-solid media is highly stringent and enables identification of the most efficient pairs. These results demonstrate that cross-feeding is a viable approach for controlling community composition within diverse synthetic communities.
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Affiliation(s)
- Erin E Kelly
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Alexandria M Fischer
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA.,Department of Biology, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Cynthia H Collins
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA.,Department of Biology, Rensselaer Polytechnic Institute, Troy, New York, USA
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12
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Oh EJ, Jin YS. Engineering of Saccharomyces cerevisiae for efficient fermentation of cellulose. FEMS Yeast Res 2021; 20:5698803. [PMID: 31917414 DOI: 10.1093/femsyr/foz089] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/08/2020] [Indexed: 12/18/2022] Open
Abstract
Conversion of lignocellulosic biomass to biofuels using microbial fermentation is an attractive option to substitute petroleum-based production economically and sustainably. The substantial efforts to design yeast strains for biomass hydrolysis have led to industrially applicable biological routes. Saccharomyces cerevisiae is a robust microbial platform widely used in biofuel production, based on its amenability to systems and synthetic biology tools. The critical challenges for the efficient microbial conversion of lignocellulosic biomass by engineered S. cerevisiae include heterologous expression of cellulolytic enzymes, co-fermentation of hexose and pentose sugars, and robustness against various stresses. Scientists developed many engineering strategies for cellulolytic S. cerevisiae strains, bringing the application of consolidated bioprocess at an industrial scale. Recent advances in the development and implementation of engineered yeast strains capable of assimilating lignocellulose will be reviewed.
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Affiliation(s)
- Eun Joong Oh
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, 4001 Discovery Dr., CO 80303, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, 905 S. Goodwin Ave., IL 61801, USA.,1105 Carl R. Woese Institute for Genomic Biology, 1206 W. Gregory Dr. Urbana, IL 61801. USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr. Urbana, IL 61801, USA
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13
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Research progress and the biotechnological applications of multienzyme complex. Appl Microbiol Biotechnol 2021; 105:1759-1777. [PMID: 33564922 DOI: 10.1007/s00253-021-11121-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/07/2021] [Accepted: 01/16/2021] [Indexed: 11/26/2022]
Abstract
The multienzyme complex system has become a research focus in synthetic biology due to its highly efficient overall catalytic ability and has been applied to various fields. Multienzyme complexes are formed by cascading complexes, which are multiple functionally related enzymes that continuously and efficiently catalyze the production of substrates. Compared with current mainstream microbial cell catalytic systems, in vitro multienzyme molecular machines have many advantages, such as fewer side reactions, a high product yield, a fast reaction speed, easy product separation, a tolerable toxic environment, and robust system operability, showing increasing competitiveness in the field of biomanufacturing. In this review, the research progress of multienzyme complexes in nature and multienzyme cascades in vivo or in vitro will be introduced, and the discovered enzyme cascades concerning scaffolding proteins will also be discussed. This review is expected to provide a more theoretical basis for the modification of multienzyme complexes and broaden their application in the field of synthetic biology. KEY POINTS: • The cascade reactions of some natural multienzyme complexes are reviewed. • The main approaches of constructing artificial multienzyme complexes are summarized. • The structure and application of cellulosomes are discussed and prospected.
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14
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Lopes AMM, Martins M, Goldbeck R. Heterologous Expression of Lignocellulose-Modifying Enzymes in Microorganisms: Current Status. Mol Biotechnol 2021; 63:184-199. [PMID: 33484441 DOI: 10.1007/s12033-020-00288-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2020] [Indexed: 02/06/2023]
Abstract
Heterologous expression of the carbohydrate-active enzymes in microorganisms is a promising approach to produce bio-based compounds, such as fuels, nutraceuticals and other value-added products from sustainable lignocellulosic sources. Several microorganisms, including Saccharomyces cerevisiae, Escherichia coli, and the filamentous fungi Aspergillus nidulans, have unique characteristics desirable for a biorefinery production approach like well-known genetic tools, thermotolerance, high fermentative capacity and product tolerance, and high amount of recombinant enzyme secretion. These microbial factories are already stablished in the heterologous production of the carbohydrate-active enzymes to produce, among others, ethanol, xylooligosaccharides and the valuable coniferol. A complete biocatalyst able to heterologous express the CAZymes of glycoside hydrolases, carbohydrate esterases and auxiliary activities families could release these compounds faster, with higher yield and specificity. Recent advances in the synthetic biology tools could expand the number and diversity of enzymes integrated in these microorganisms, and also modify those already integrated. This review outlines the heterologous expression of carbohydrate-active enzymes in microorganisms, as well as recent updates in synthetic biology.
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Affiliation(s)
- Alberto Moura Mendes Lopes
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Rua Monteiro Lobato no 80, Cidade Universitária, Campinas, São Paulo, 13083-862, Brazil
| | - Manoela Martins
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Rua Monteiro Lobato no 80, Cidade Universitária, Campinas, São Paulo, 13083-862, Brazil
| | - Rosana Goldbeck
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Rua Monteiro Lobato no 80, Cidade Universitária, Campinas, São Paulo, 13083-862, Brazil.
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15
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Ye M, Ye Y, Du Z, Chen G. Cell-surface engineering of yeasts for whole-cell biocatalysts. Bioprocess Biosyst Eng 2021; 44:1003-1019. [PMID: 33389168 DOI: 10.1007/s00449-020-02484-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/16/2020] [Indexed: 01/23/2023]
Abstract
Due to the unique advantages comparing with traditional free enzymes and chemical catalysis, whole-cell biocatalysts have been widely used to catalyze reactions effectively, simply and environment friendly. Cell-surface display technology provides a novel and effective approach for improved whole-cell biocatalysts expressing heterologous enzymes on the cell surface. They can overcome the substrate transport limitation of the intracellular expression and provide the enzymes with enhanced properties. Among all the host surface-displaying microorganisms, yeast is ideally suitable for constructing whole cell-surface-displaying biocatalyst, because of the large cell size, the generally regarded as safe (GRAS) status, and the perfect post-translational processing of secreted proteins. Yeast cell-surface display system has been a promising and powerful method for development of novel and improved engineered biocatalysts. In this review, the characterization and principles of yeast cell-surface display and the applications of yeast cell-surface display in engineered whole-cell biocatalysts as well as the improvement of the enzyme efficiency are summarized and discussed.
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Affiliation(s)
- Mengqi Ye
- Marine College, Shandong University, Weihai, 264209, China
| | - Yuqi Ye
- Marine College, Shandong University, Weihai, 264209, China
| | - Zongjun Du
- Marine College, Shandong University, Weihai, 264209, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Guanjun Chen
- Marine College, Shandong University, Weihai, 264209, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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16
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Abstract
Cellulosomes are elaborate multienzyme complexes capable of efficiently deconstructing lignocellulosic substrates, produced by cellulolytic anaerobic microorganisms, colonizing a large variety of ecological niches. These macromolecular structures have a modular architecture and are composed of two main elements: the cohesin-bearing scaffoldins, which are non-catalytic structural proteins, and the various dockerin-bearing enzymes that tenaciously bind to the scaffoldins. Cellulosome assembly is mediated by strong and highly specific interactions between the cohesin modules, present in the scaffoldins, and the dockerin modules, present in the catalytic units. Cellulosomal architecture and composition varies between species and can even change within the same organism. These differences seem to be largely influenced by external factors, including the nature of the available carbon-source. Even though cellulosome producing organisms are relatively few, the development of new genomic and proteomic technologies has allowed the identification of cellulosomal components in many archea, bacteria and even some primitive eukaryotes. This reflects the importance of this cellulolytic strategy and suggests that cohesin-dockerin interactions could be involved in other non-cellulolytic processes. Due to their building-block nature and highly cellulolytic capabilities, cellulosomes hold many potential biotechnological applications, such as the conversion of lignocellulosic biomass in the production of biofuels or the development of affinity based technologies.
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Affiliation(s)
- Victor D Alves
- CIISA, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal
| | - Carlos M G A Fontes
- CIISA, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal
| | - Pedro Bule
- CIISA, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal.
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17
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Vanderstraeten J, Briers Y. Synthetic protein scaffolds for the colocalisation of co-acting enzymes. Biotechnol Adv 2020; 44:107627. [DOI: 10.1016/j.biotechadv.2020.107627] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
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18
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Ding Q, Diao W, Gao C, Chen X, Liu L. Microbial cell engineering to improve cellular synthetic capacity. Biotechnol Adv 2020; 45:107649. [PMID: 33091485 DOI: 10.1016/j.biotechadv.2020.107649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/02/2020] [Accepted: 10/13/2020] [Indexed: 01/21/2023]
Abstract
Rapid technological progress in gene assembly, biosensors, and genetic circuits has led to reinforce the cellular synthetic capacity for chemical production. However, overcoming the current limitations of these techniques in maintaining cellular functions and enhancing the cellular synthetic capacity (e.g., catalytic efficiency, strain performance, and cell-cell communication) remains challenging. In this review, we propose a strategy for microbial cell engineering to improve the cellular synthetic capacity by utilizing biotechnological tools along with system biology methods to regulate cellular functions during chemical production. Current strategies in microbial cell engineering are mainly focused on the organelle, cell, and consortium levels. This review highlights the potential of using biotechnology to further develop the field of microbial cell engineering and provides guidance for utilizing microorganisms as attractive regulation targets.
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Affiliation(s)
- Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wenwen Diao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
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19
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Dong C, Qiao J, Wang X, Sun W, Chen L, Li S, Wu K, Ma L, Liu Y. Engineering Pichia pastoris with surface-display minicellulosomes for carboxymethyl cellulose hydrolysis and ethanol production. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:108. [PMID: 32549912 PMCID: PMC7296672 DOI: 10.1186/s13068-020-01749-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUNDS Engineering yeast as a consolidated bioprocessing (CBP) microorganism by surface assembly of cellulosomes has been aggressively utilized for cellulosic ethanol production. However, most of the previous studies focused on Saccharomyces cerevisiae, achieving efficient conversion of phosphoric acid-swollen cellulose (PASC) or microcrystalline cellulose (Avicel) but not carboxymethyl cellulose (CMC) to ethanol, with an average titer below 2 g/L. RESULTS Harnessing an ultra-high-affinity IM7/CL7 protein pair, here we describe a method to engineer Pichia pastoris with minicellulosomes by in vitro assembly of three recombinant cellulases including an endoglucanase (EG), an exoglucanase (CBH) and a β-glucosidase (BGL), as well as a carbohydrate-binding module (CBM) on the cell surface. For the first time, the engineered yeasts enable efficient and direct conversion of CMC to bioethanol, observing an impressive ethanol titer of 5.1 g/L. CONCLUSIONS The research promotes the application of P. pastoris as a CBP cell factory in cellulosic ethanol production and provides a promising platform for screening the cellulases from different species to construct surface-assembly celluosome.
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Affiliation(s)
- Ce Dong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Jie Qiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Xinping Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Wenli Sun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Lixia Chen
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Shuntang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Ke Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
- BravoVax Co., Ltd., Wuhan, 430000 Hubei China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Yi Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
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20
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Dinh CV, Chen X, Prather KLJ. Development of a Quorum-Sensing Based Circuit for Control of Coculture Population Composition in a Naringenin Production System. ACS Synth Biol 2020; 9:590-597. [PMID: 32040906 DOI: 10.1021/acssynbio.9b00451] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As synthetic biology and metabolic engineering tools improve, it is feasible to construct more complex microbial synthesis systems that may be limited by the machinery and resources available in an individual cell. Coculture fermentation is a promising strategy for overcoming these constraints by distributing objectives between subpopulations, but the primary method for controlling the composition of the coculture of production systems has been limited to control of the inoculum composition. We have developed a quorum sensing (QS)-based growth-regulation circuit that provides an additional parameter for regulating the composition of a coculture over the course of the fermentation. Implementation of this tool in a naringenin-producing coculture resulted in a 60% titer increase over a system that was optimized by varying inoculation ratios only. We additionally demonstrated that the growth control circuit can be implemented in combination with a communication module that couples transcription in one subpopulation to the cell-density of the other population for coordination of behavior, resulting in an additional 60% improvement in naringenin titer.
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Affiliation(s)
- Christina V Dinh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Xingyu Chen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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21
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Klein WP, Thomsen RP, Turner KB, Walper SA, Vranish J, Kjems J, Ancona MG, Medintz IL. Enhanced Catalysis from Multienzyme Cascades Assembled on a DNA Origami Triangle. ACS NANO 2019; 13:13677-13689. [PMID: 31751123 DOI: 10.1021/acsnano.9b05746] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Developing reliable methods of constructing cell-free multienzyme biocatalytic systems is a milestone goal of synthetic biology. It would enable overcoming the limitations of current cell-based systems, which suffer from the presence of competing pathways, toxicity, and inefficient access to extracellular reactants and removal of products. DNA nanostructures have been suggested as ideal scaffolds for assembling sequential enzymatic cascades in close enough proximity to potentially allow for exploiting of channeling effects; however, initial demonstrations have provided somewhat contradictory results toward confirming this phenomenon. In this work, a three-enzyme sequential cascade was realized by site-specifically immobilizing DNA-conjugated amylase, maltase, and glucokinase on a self-assembled DNA origami triangle. The kinetics of seven different enzyme configurations were evaluated experimentally and compared to simulations of optimized activity. A 30-fold increase in the pathway's kinetic activity was observed for enzymes assembled to the DNA. Detailed kinetic analysis suggests that this catalytic enhancement originated from increased enzyme stability and a localized DNA surface affinity or hydration layer effect and not from a directed enzyme-to-enzyme channeling mechanism. Nevertheless, the approach used to construct this pathway still shows promise toward improving other more elaborate multienzymatic cascades and could potentially allow for the custom synthesis of complex (bio)molecules that cannot be realized with conventional organic chemistry approaches.
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Affiliation(s)
- William P Klein
- National Research Council , Washington , D.C. 20001 , United States
| | - Rasmus P Thomsen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics , Aarhus University , 8000 Aarhus , Denmark
| | | | - Scott A Walper
- National Research Council , Washington , D.C. 20001 , United States
| | - James Vranish
- Ave Maria University , Ave Maria , Florida 34142 , United States
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics , Aarhus University , 8000 Aarhus , Denmark
| | | | - Igor L Medintz
- National Research Council , Washington , D.C. 20001 , United States
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22
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Losoi PS, Santala VP, Santala SM. Enhanced Population Control in a Synthetic Bacterial Consortium by Interconnected Carbon Cross-Feeding. ACS Synth Biol 2019; 8:2642-2650. [PMID: 31751122 DOI: 10.1021/acssynbio.9b00316] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Engineered microbial consortia can provide several advantages over monocultures in terms of utilization of mixed substrates, resistance to perturbations, and division of labor in complex tasks. However, maintaining stability, reproducibility, and control over population levels in variable conditions can be challenging in multispecies cultures. In our study, we modeled and constructed a synthetic symbiotic consortium with a genetically encoded carbon cross-feeding system. The system is based on strains of Escherichia coli and Acinetobacter baylyi ADP1, both engineered to be incapable of growing on glucose on their own. In a culture supplemented with glucose as the sole carbon source, growth of the two strains is afforded by the exchange of gluconate and acetate, resulting in inherent control over carbon availability and population balance. We investigated the system robustness in terms of stability and population control under different inoculation ratios, substrate concentrations, and cultivation scales, both experimentally and by modeling. To illustrate how the system might facilitate division of genetic circuits among synthetic microbial consortia, a green fluorescent protein sensitive to pH and a slowly maturing red fluorescent protein were expressed in the consortium as measures of a circuit's susceptibility to external and internal variability, respectively. The symbiotic consortium maintained stable and linear growth and circuit performance regardless of the initial substrate concentration or inoculation ratio. The developed cross-feeding system provides simple and reliable means for population control without expression of non-native elements or external inducer addition, being potentially exploitable in consortia applications involving precisely defined cell tasks or division of labor.
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Affiliation(s)
- Pauli S. Losoi
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta campus, Korkeakoulunkatu 8, Tampere, 33720, Finland
| | - Ville P. Santala
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta campus, Korkeakoulunkatu 8, Tampere, 33720, Finland
| | - Suvi M. Santala
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta campus, Korkeakoulunkatu 8, Tampere, 33720, Finland
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23
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Ellis GA, Klein WP, Lasarte-Aragonés G, Thakur M, Walper SA, Medintz IL. Artificial Multienzyme Scaffolds: Pursuing in Vitro Substrate Channeling with an Overview of Current Progress. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02413] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - William P. Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20001, United States
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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24
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Stephens K, Pozo M, Tsao CY, Hauk P, Bentley WE. Bacterial co-culture with cell signaling translator and growth controller modules for autonomously regulated culture composition. Nat Commun 2019; 10:4129. [PMID: 31511505 PMCID: PMC6739400 DOI: 10.1038/s41467-019-12027-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/14/2019] [Indexed: 12/21/2022] Open
Abstract
Synthetic biology and metabolic engineering have expanded the possibilities for engineered cell-based systems. The addition of non-native biosynthetic and regulatory components can, however, overburden the reprogrammed cells. In order to avoid metabolic overload, an emerging area of focus is on engineering consortia, wherein cell subpopulations work together to carry out a desired function. This strategy requires regulation of the cell populations. Here, we design a synthetic co-culture controller consisting of cell-based signal translator and growth-controller modules that, when implemented, provide for autonomous regulation of the consortia composition. The system co-opts the orthogonal autoinducer AI-1 and AI-2 cell-cell signaling mechanisms of bacterial quorum sensing (QS) to enable cross-talk between strains and a QS signal-controlled growth rate controller to modulate relative population densities. We further develop a simple mathematical model that enables cell and system design for autonomous closed-loop control of population trajectories. To avoid metabolic overload and divide tasks, synthetic biologists are turning to microbial consortia engineering. Here the authors design a co-culture controller that autonomously regulates population composition.
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Affiliation(s)
- Kristina Stephens
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA
| | - Maria Pozo
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA
| | - Chen-Yu Tsao
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA
| | - Pricila Hauk
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA. .,Institute for Bioscience and Biotechnology Research, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA.
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25
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Hu B, Zhu M. Reconstitution of cellulosome: Research progress and its application in biorefinery. Biotechnol Appl Biochem 2019; 66:720-730. [DOI: 10.1002/bab.1804] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/03/2019] [Indexed: 09/01/2023]
Affiliation(s)
- Bin‐Bin Hu
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals School of Biology and Biological Engineering South China University of Technology, Guangzhou Higher Education Mega Center Panyu Guangzhou People's Republic of China
- Yunnan Academy of Tobacco Agricultural Sciences Kunming People's Republic of China
- State Key Laboratory of Pulp and Paper Engineering South China University of Technology Guangzhou People's Republic of China
| | - Ming‐Jun Zhu
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals School of Biology and Biological Engineering South China University of Technology, Guangzhou Higher Education Mega Center Panyu Guangzhou People's Republic of China
- State Key Laboratory of Pulp and Paper Engineering South China University of Technology Guangzhou People's Republic of China
- College of Life and Geographic Sciences Kashi University Kashi People's Republic of China
- The Key Laboratory of Ecology and Biological Resources in Yarkand Oasis at Colleges & Universities under the Department of Education of Xinjiang Uygur Autonomous Region Kashi University Kashi People's Republic of China
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26
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Wang Y, Leng L, Islam MK, Liu F, Lin CSK, Leu SY. Substrate-Related Factors Affecting Cellulosome-Induced Hydrolysis for Lignocellulose Valorization. Int J Mol Sci 2019; 20:ijms20133354. [PMID: 31288425 PMCID: PMC6651384 DOI: 10.3390/ijms20133354] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/30/2019] [Accepted: 07/03/2019] [Indexed: 11/22/2022] Open
Abstract
Cellulosomes are an extracellular supramolecular multienzyme complex that can efficiently degrade cellulose and hemicelluloses in plant cell walls. The structural and unique subunit arrangement of cellulosomes can promote its adhesion to the insoluble substrates, thus providing individual microbial cells with a direct competence in the utilization of cellulosic biomass. Significant progress has been achieved in revealing the structures and functions of cellulosomes, but a knowledge gap still exists in understanding the interaction between cellulosome and lignocellulosic substrate for those derived from biorefinery pretreatment of agricultural crops. The cellulosomic saccharification of lignocellulose is affected by various substrate-related physical and chemical factors, including native (untreated) wood lignin content, the extent of lignin and xylan removal by pretreatment, lignin structure, substrate size, and of course substrate pore surface area or substrate accessibility to cellulose. Herein, we summarize the cellulosome structure, substrate-related factors, and regulatory mechanisms in the host cells. We discuss the latest advances in specific strategies of cellulosome-induced hydrolysis, which can function in the reaction kinetics and the overall progress of biorefineries based on lignocellulosic feedstocks.
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Affiliation(s)
- Ying Wang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Ling Leng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Md Khairul Islam
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Fanghua Liu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Shao-Yuan Leu
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
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27
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Jiang Y, Wu R, Zhou J, He A, Xu J, Xin F, Zhang W, Ma J, Jiang M, Dong W. Recent advances of biofuels and biochemicals production from sustainable resources using co-cultivation systems. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:155. [PMID: 31285755 PMCID: PMC6588928 DOI: 10.1186/s13068-019-1495-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 06/11/2019] [Indexed: 05/09/2023]
Abstract
Microbial communities are ubiquitous in nature and exhibit several attractive features, such as sophisticated metabolic capabilities and strong environment robustness. Inspired by the advantages of natural microbial consortia, diverse artificial co-cultivation systems have been metabolically constructed for biofuels, chemicals and natural products production. In these co-cultivation systems, especially genetic engineering ones can reduce the metabolic burden caused by the complex of metabolic pathway through labor division, and improve the target product production significantly. This review summarized the most up-to-dated co-cultivation systems used for biofuels, chemicals and nature products production. In addition, major challenges associated with co-cultivation systems are also presented and discussed for meeting further industrial demands.
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Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
| | - Ruofan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Aiyong He
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, 223300 People’s Republic of China
| | - Jiaxing Xu
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, 223300 People’s Republic of China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
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Engineering the early secretory pathway for increased protein secretion in Saccharomyces cerevisiae. Metab Eng 2019; 55:142-151. [PMID: 31220665 DOI: 10.1016/j.ymben.2019.06.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/31/2019] [Accepted: 06/17/2019] [Indexed: 11/21/2022]
Abstract
The yeast Saccharomyces cerevisiae is a valuable host for the production of heterologous proteins with a wide array of applications, ranging from cellulose saccharification enzymes to biopharmaceuticals. Efficient protein secretion may be critical for economic viability; however previous efforts have shown limited improvements that are often protein-specific. By enhancing transit through the early secretory pathway, we have successfully improved extracellular levels of three different proteins from variety of origins: a bacterial endoglucanase (CelA), a fungal β-glucosidase (BglI) and a single-chain antibody fragment (4-4-20 scFv). Efficient co-translational translocation into the endoplasmic reticulum (ER) was achieved via secretion peptide engineering and the novel use of a 3'-untranslated region, improving extracellular activity or fluorescence 2.2-5.4-fold. We further optimized the pathway using a variety of new strategies including: i) increasing secretory pathway capacity by expanding the ER, ii) limiting ER-associated degradation, and iii) enhancing exit from the ER. By addressing these additional ER processing steps, extracellular activity/fluorescence increased by 3.5-7.1-fold for the three diverse proteins. The optimal combination of pathway interventions varied, and the highest overall increases ranged from 5.8 to 11-fold. These successful strategies should prove effective for improving the secretion of a wide range of heterologous proteins.
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Lu L, Zhang L, Yuan L, Zhu T, Chen W, Wang G, Wang Q. Artificial Cellulosome Complex from the Self-Assembly of Ni-NTA-Functionalized Polymeric Micelles and Cellulases. Chembiochem 2019; 20:1394-1399. [PMID: 30697892 DOI: 10.1002/cbic.201900061] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Indexed: 12/17/2023]
Abstract
Polymer-protein core-shell nanoparticles have been explored for enzyme immobilization. This work reports on the development of functional polymeric micelles for immobilizing His6 -tagged cellulases with controlled spatial orientation of enzymes, resulting in "artificial cellulosomes" for effective cellulose hydrolysis. Poly(styrene)-b-poly(styrene-alt-maleic anhydride) was prepared through one-pot reversible addition-fragmentation chain-transfer polymerization and modified with nitrilotriacetic acid (NTA) to afford an amphiphilic block copolymer. The self-assembled polymer was mixed with a solution of NiSO4 to form Ni-NTA-functionalized micelles, which could successfully capture His6 -tagged cellulases and form hierarchically structured core-shell nanoparticles with cellulases as the corona. Because the anchored enzymes are site-specifically oriented and in close proximity, synergistic catalysis that results in over twofold activity enhancement has been achieved.
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Affiliation(s)
- Lin Lu
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Libo Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Liang Yuan
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Tianyu Zhu
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE, 19716, USA
| | - Guiren Wang
- Department of Mechanical Engineering, University of South Carolina, 301 Main Street, Columbia, SC, 29208, USA
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
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30
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Yang X, Tang H, Song M, Shen Y, Hou J, Bao X. Development of novel surface display platforms for anchoring heterologous proteins in Saccharomyces cerevisiae. Microb Cell Fact 2019; 18:85. [PMID: 31103030 PMCID: PMC6525377 DOI: 10.1186/s12934-019-1133-x] [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: 03/06/2019] [Accepted: 05/07/2019] [Indexed: 01/29/2023] Open
Abstract
Background Cell surface display of recombinant proteins has become a powerful tool for biotechnology and biomedical applications. As a model eukaryotic microorganism, Saccharomyces cerevisiae is an ideal candidate for surface display of heterologous proteins. However, the frequently used commercial yeast surface display system, the a-agglutinin anchor system, often results in low display efficiency. Results We initially reconstructed the a-agglutinin system by replacing two anchor proteins with one anchor protein. By directly fusing the target protein to the N-terminus of Aga1p and inserting a flexible linker, the display efficiency almost doubled, and the activity of reporter protein α-galactosidase increased by 39%. We also developed new surface display systems. Six glycosylphosphatidylinositol (GPI) anchored cell wall proteins were selected to construct the display systems. Among them, Dan4p and Sed1p showed higher display efficiency than the a-agglutinin anchor system. Linkers were also inserted to eliminate the effects of GPI fusion on the activity of the target protein. We further used the newly developed Aga1p, Dan4p systems and Sed1p system to display exoglucanase and a relatively large protein β-glucosidase, and found that Aga1p and Dan4p were more suitable for immobilizing large proteins. Conclusion Our study developed novel efficient yeast surface display systems, that will be attractive tools for biotechnological and biomedical applications Electronic supplementary material The online version of this article (10.1186/s12934-019-1133-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoyu Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Hongting Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.,Center for Synthetic Biochemistry, Chinese Academy of Sciences, Shenzhen Institutes for Advanced Technologies, Shenzhen, 518055, People's Republic of China
| | - Meihui Song
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China. .,Shandong Provincial Key Laboratory of Microbial Engineering, Qi Lu University of Technology, Jinan, 250353, People's Republic of China.
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Heterologous co-expression of two β-glucanases and a cellobiose phosphorylase resulted in a significant increase in the cellulolytic activity of the Caldicellulosiruptor bescii exoproteome. J Ind Microbiol Biotechnol 2019; 46:687-695. [PMID: 30783893 DOI: 10.1007/s10295-019-02150-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/12/2019] [Indexed: 12/20/2022]
Abstract
The ability to deconstruct plant biomass without conventional pretreatment has made members of the genus Caldicellulosiruptor the target of investigation for the consolidated processing of plant lignocellulosic biomass to biofuels and bioproducts. To investigate the synergy of enzymes involved and to further improve the ability of C. bescii to degrade cellulose, we introduced CAZymes that act synergistically with the C. bescii exoproteome in vivo and in vitro. We recently demonstrated that the Acidothermus cellulolyticus E1 endo-1,4-β-D-glucanase (GH5) with a family 2 carbohydrate-binding module (CBM) increased the activity of C. bescii exoproteome on biomass, presumably acting in concert with CelA. The β-glucanase, GuxA, from A. cellulolyticus is a multi-domain enzyme with strong processive exoglucanase activity, and the cellobiose phosphorylase from Thermotoga maritima catalyzes cellulose degradation acting synergistically with cellobiohydrolases and endoglucanases. We identified new chromosomal insertion sites to co-express these enzymes and the resulting strain showed a significant increase in the enzymatic activity of the exoproteome.
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32
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McCarty NS, Ledesma-Amaro R. Synthetic Biology Tools to Engineer Microbial Communities for Biotechnology. Trends Biotechnol 2019; 37:181-197. [PMID: 30497870 PMCID: PMC6340809 DOI: 10.1016/j.tibtech.2018.11.002] [Citation(s) in RCA: 225] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022]
Abstract
Microbial consortia have been used in biotechnology processes, including fermentation, waste treatment, and agriculture, for millennia. Today, synthetic biologists are increasingly engineering microbial consortia for diverse applications, including the bioproduction of medicines, biofuels, and biomaterials from inexpensive carbon sources. An improved understanding of natural microbial ecosystems, and the development of new tools to construct synthetic consortia and program their behaviors, will vastly expand the functions that can be performed by communities of interacting microorganisms. Here, we review recent advancements in synthetic biology tools and approaches to engineer synthetic microbial consortia, discuss ongoing and emerging efforts to apply consortia for various biotechnological applications, and suggest future applications.
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Affiliation(s)
- Nicholas S. McCarty
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- 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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Abstract
Proteins are not designed to be standalone entities and must coordinate their collective action for optimum performance. Nature has developed through evolution the ability to colocalize the functional partners of a cascade enzymatic reaction in order to ensure efficient exchange of intermediates. Inspired by these natural designs, synthetic scaffolds have been created to enhance the overall biological pathway performance. In this chapter, we describe several DNA- and protein-based scaffold approaches to assemble artificial enzyme cascades for a wide range of applications. We highlight the key benefits and drawbacks of these approaches to provide insights on how to choose the appropriate scaffold for different cascade systems.
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Affiliation(s)
- Qing Sun
- Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei City, Taiwan
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States.
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Kalbarczyk KZ, Mazeau EJ, Rapp KM, Marchand N, Koffas MAG, Collins CH. Engineering Bacillus megaterium Strains To Secrete Cellulases for Synergistic Cellulose Degradation in a Microbial Community. ACS Synth Biol 2018; 7:2413-2422. [PMID: 30226981 DOI: 10.1021/acssynbio.8b00186] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recent environmental concerns have intensified the need to develop systems to degrade waste biomass for use as an inexpensive carbon source for microbial chemical production. Current approaches to biomass utilization rely on pretreatment processes that include expensive enzymatic purification steps for the requisite cellulases. We aimed to engineer a synthetic microbial community to synergistically degrade cellulose by compartmentalizing the system with multiple specialized Bacillus megaterium strains. EGI1, an endoglucanase, and Cel9AT, a multimodular cellulase, were targeted for secretion from B. megaterium. A small library of signal peptides (SPs) with five amino acid linkers was selected to tag each cellulase for secretion from B. megaterium. Cellulase activity against amorphous cellulose was confirmed through a series of bioassays, and the most active SP constructs were identified as EGI1 with the LipA SP and Cel9AT with the YngK SP. The activity of the optimized cellulase secretion strains was characterized individually and in tandem to assess synergistic cellulolytic activity. The combination of EGI1 and Cel9AT yielded higher activity than either single cellulase. A coculture of EGI1 and Cel9AT secreting B. megaterium strains demonstrated synergistic behavior with higher activity than either monoculture. This cellulose degradation module can be further integrated with bioproduct synthesis modules to build complex systems for the production of high value molecules.
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Affiliation(s)
- Karolina Z. Kalbarczyk
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Emily J. Mazeau
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Kent M. Rapp
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Nicholas Marchand
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Mattheos A. G. Koffas
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Cynthia H. Collins
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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Tang H, Wang J, Wang S, Shen Y, Petranovic D, Hou J, Bao X. Efficient yeast surface-display of novel complex synthetic cellulosomes. Microb Cell Fact 2018; 17:122. [PMID: 30086751 PMCID: PMC6081942 DOI: 10.1186/s12934-018-0971-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/01/2018] [Indexed: 11/12/2022] Open
Abstract
Background The self-assembly of cellulosomes on the surface of yeast is a promising strategy for consolidated bioprocessing to convert cellulose into ethanol in one step. Results In this study, we developed a novel synthetic cellulosome that anchors to the endogenous yeast cell wall protein a-agglutinin through disulfide bonds. A synthetic scaffoldin ScafAGA3 was constructed using the repeated N-terminus of Aga1p and displayed on the yeast cell surface. Secreted cellulases were then fused with Aga2p to assemble the cellulosome. The display efficiency of the synthetic scaffoldin and the assembly efficiency of each enzyme were much higher than those of the most frequently constructed cellulosome using scaffoldin ScafCipA3 from Clostridium thermocellum. A complex cellulosome with two scaffoldins was also constructed using interactions between the displayed anchoring scaffoldin ScafAGA3 and scaffoldin I ScafCipA3 through disulfide bonds, and the assembly of secreted cellulases to ScafCipA3. The newly designed cellulosomes enabled yeast to directly ferment cellulose into ethanol. Conclusions This is the first report on the development of complex multiple-component assembly system through disulfide bonds. This strategy could facilitate the construction of yeast cell factories to express synergistic enzymes for use in biotechnology. Electronic supplementary material The online version of this article (10.1186/s12934-018-0971-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongting Tang
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, Qingdao, 266237, People's Republic of China
| | - Jiajing Wang
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, Qingdao, 266237, People's Republic of China
| | - Shenghuan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, Qingdao, 266237, People's Republic of China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, Qingdao, 266237, People's Republic of China
| | - Dina Petranovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 41296, Gothenburg, Sweden
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, Qingdao, 266237, People's Republic of China.
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, Qingdao, 266237, People's Republic of China. .,Shandong Provincial Key Laboratory of Microbial Engineering, Qi Lu University of Technology, Jinan, 250353, People's Republic of China.
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36
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Tabañag IDF, Chu IM, Wei YH, Tsai SL. Ethanol production from hemicellulose by a consortium of different genetically-modified sacharomyces cerevisiae. J Taiwan Inst Chem Eng 2018. [DOI: 10.1016/j.jtice.2018.04.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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37
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Padkina MV, Sambuk EV. Prospects for the Application of Yeast Display in Biotechnology and Cell Biology (Review). APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818040105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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38
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Chen L, Du JL, Zhan YJ, Li JA, Zuo RR, Tian S. Consolidated bioprocessing for cellulosic ethanol conversion by cellulase-xylanase cell-surfaced yeast consortium. Prep Biochem Biotechnol 2018; 48:653-661. [PMID: 29995567 DOI: 10.1080/10826068.2018.1487846] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Consolidated bioprocessing (CBP) strategy was developed to construct a cell-surface displayed consortium for heterologously expressing functional lignocellulytic enzymes. The reaction system composed of two engineered yeast strains: Y5/XynII-XylA (co-displaying two types of xylanases) and Y5/EG-CBH-BGL (co-displaying three types of cellulases). The immobilization of recombinant fusion proteins and their cell-surface accessibility of were analyzed by flow cytometry and immunofluorescence. The feasibility of consolidated bioprocessing by using pretreated corn stover (CS) as substrate for direct bioconversion was further investigated, and the synergistic activity and proximity effect between cellulases and xylanases on lignocelluloses degradation were also discussed in this work. Without any commercial enzyme addition, the combined yeast consortium produced 1.61 g/L ethanol which achieved 64.7% of the theoretical ethanol yield during 144 h from steam-exploded CS. The results indicated that the assembly of cellulases and xylanases using a synthetic consortium capable of combined displaying lignocellulytic enzymes is a promising approach for simultaneous saccharification and fermentation to ethanol from lignocellulosic biomass.
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Affiliation(s)
- Le Chen
- a College of Life Science , Capital Normal University , Beijing , China
| | - Ji-Liang Du
- a College of Life Science , Capital Normal University , Beijing , China
| | - Yong-Jia Zhan
- a College of Life Science , Capital Normal University , Beijing , China
| | - Jian-An Li
- a College of Life Science , Capital Normal University , Beijing , China
| | - Ran-Ran Zuo
- a College of Life Science , Capital Normal University , Beijing , China
| | - Shen Tian
- a College of Life Science , Capital Normal University , Beijing , China
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39
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Tools for engineering coordinated system behaviour in synthetic microbial consortia. Nat Commun 2018; 9:2677. [PMID: 29992956 PMCID: PMC6041260 DOI: 10.1038/s41467-018-05046-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/11/2018] [Indexed: 12/02/2022] Open
Abstract
Advancing synthetic biology to the multicellular level requires the development of multiple cell-to-cell communication channels that propagate information with minimal signal interference. The development of quorum-sensing devices, the cornerstone technology for building microbial communities with coordinated system behaviour, has largely focused on cognate acyl-homoserine lactone (AHL)/transcription factor pairs, while the use of non-cognate pairs as a design feature has received limited attention. Here, we demonstrate a large library of AHL-receiver devices, with all cognate and non-cognate chemical signal interactions quantified, and we develop a software tool that automatically selects orthogonal communication channels. We use this approach to identify up to four orthogonal channels in silico, and experimentally demonstrate the simultaneous use of three channels in co-culture. The development of multiple non-interfering cell-to-cell communication channels is an enabling step that facilitates the design of synthetic consortia for applications including distributed bio-computation, increased bioprocess efficiency, cell specialisation and spatial organisation. The engineering of synthetic microbial communities necessitates the use of synthetic, orthogonal cell-to-cell communication channels. Here the authors present a library of characterised AHL-receiver devices and a software tool for the automatic identification of non-interfering chemical communication channels.
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40
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Stern J, Moraïs S, Ben-David Y, Salama R, Shamshoum M, Lamed R, Shoham Y, Bayer EA, Mizrahi I. Assembly of Synthetic Functional Cellulosomal Structures onto the Cell Surface of Lactobacillus plantarum, a Potent Member of the Gut Microbiome. Appl Environ Microbiol 2018; 84:e00282-18. [PMID: 29453253 PMCID: PMC5881048 DOI: 10.1128/aem.00282-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 12/27/2022] Open
Abstract
Heterologous display of enzymes on microbial cell surfaces is an extremely desirable approach, since it enables the engineered microbe to interact directly with the plant wall extracellular polysaccharide matrix. In recent years, attempts have been made to endow noncellulolytic microbes with genetically engineered cellulolytic capabilities for improved hydrolysis of lignocellulosic biomass and for advanced probiotics. Thus far, however, owing to the hurdles encountered in secreting and assembling large, intricate complexes on the bacterial cell wall, only free cellulases or relatively simple cellulosome assemblies have been introduced into live bacteria. Here, we employed the "adaptor scaffoldin" strategy to compensate for the low levels of protein displayed on the bacterial cell surface. That strategy mimics natural elaborated cellulosome architectures, thus exploiting the exponential features of their Lego-like combinatorics. Using this approach, we produced several bacterial consortia of Lactobacillus plantarum, a potent gut microbe which provides a very robust genetic framework for lignocellulosic degradation. We successfully engineered surface display of large, fully active self-assembling cellulosomal complexes containing an unprecedented number of catalytic subunits all produced in vivo by the cell consortia. Our results demonstrate that the enzyme stability and performance of the cellulosomal machinery, which are superior to those seen with the equivalent secreted free enzyme system, and the high cellulase-to-xylanase ratios proved beneficial for efficient degradation of wheat straw.IMPORTANCE The multiple benefits of lactic acid bacteria are well established in health and industry. Here we present an approach designed to extensively increase the cell surface display of proteins via successive assembly of interactive components. Our findings present a stepping stone toward proficient engineering of Lactobacillus plantarum, a widespread, environmentally important bacterium and potent microbiome member, for improved degradation of lignocellulosic biomass and advanced probiotics.
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Affiliation(s)
- Johanna Stern
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yonit Ben-David
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Rachel Salama
- Department of Biotechnology and Food Engineering, The Technion Israel Institute of Technology, Haifa, Israel
| | - Melina Shamshoum
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, The Technion Israel Institute of Technology, Haifa, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Itzhak Mizrahi
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Hennig S, Wenzel M, Haas C, Hoffmann A, Weber J, Rödel G, Ostermann K. New approaches in bioprocess-control: Consortium guidance by synthetic cell-cell communication based on fungal pheromones. Eng Life Sci 2018; 18:387-400. [PMID: 32624919 DOI: 10.1002/elsc.201700181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/08/2018] [Accepted: 03/13/2018] [Indexed: 01/02/2023] Open
Abstract
Bioconversions in industrial processes are currently dominated by single-strain approaches. With the growing complexity of tasks to be carried out, microbial consortia become increasingly advantageous and eventually may outperform single-strain fermentations. Consortium approaches benefit from the combined metabolic capabilities of highly specialized strains and species, and the inherent division of labor reduces the metabolic burden for each strain while increasing product yields and reaction specificities. However, consortium-based designs still suffer from a lack of available tools to control the behavior and performance of the individual subpopulations and of the entire consortium. Here, we propose to implement novel control elements for microbial consortia based on artificial cell-cell communication via fungal mating pheromones. Coupling to the desired output is mediated by pheromone-responsive gene expression, thereby creating pheromone-dependent communication channels between different subpopulations of the consortia. We highlight the benefits of artificial communication to specifically target individual subpopulations of microbial consortia and to control e.g. their metabolic profile or proliferation rate in a predefined and customized manner. Due to the steadily increasing knowledge of sexual cycles of industrially relevant fungi, a growing number of strains and species can be integrated into pheromone-controlled sensor-actor systems, exploiting their unique metabolic properties for microbial consortia approaches.
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Affiliation(s)
- Stefan Hennig
- Institute of Genetics Technische Universität Dresden Dresden Germany
| | - Mandy Wenzel
- Institute of Genetics Technische Universität Dresden Dresden Germany
| | - Christiane Haas
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Andreas Hoffmann
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Jost Weber
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany.,Evolva Biotec A/S Lersø Parkallé 42 Copenhagen Denmark
| | - Gerhard Rödel
- Institute of Genetics Technische Universität Dresden Dresden Germany
| | - Kai Ostermann
- Institute of Genetics Technische Universität Dresden Dresden Germany
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Liu H, Sun J, Chang JS, Shukla P. Engineering microbes for direct fermentation of cellulose to bioethanol. Crit Rev Biotechnol 2018; 38:1089-1105. [DOI: 10.1080/07388551.2018.1452891] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Hao Liu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, China
| | - Jianliang Sun
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, China
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan, China
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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43
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The Role of Yeast-Surface-Display Techniques in Creating Biocatalysts for Consolidated BioProcessing. Catalysts 2018. [DOI: 10.3390/catal8030094] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Climate change is directly linked to the rapid depletion of our non-renewable fossil resources and has posed concerns on sustainability. Thus, imploring the need for us to shift from our fossil based economy to a sustainable bioeconomy centered on biomass utilization. The efficient bioconversion of lignocellulosic biomass (an ideal feedstock) to a platform chemical, such as bioethanol, can be achieved via the consolidated bioprocessing technology, termed yeast surface engineering, to produce yeasts that are capable of this feat. This approach has various strategies that involve the display of enzymes on the surface of yeast to degrade the lignocellulosic biomass, then metabolically convert the degraded sugars directly into ethanol, thus elevating the status of yeast from an immobilization material to a whole-cell biocatalyst. The performance of the engineered strains developed from these strategies are presented, visualized, and compared in this article to highlight the role of this technology in moving forward to our quest against climate change. Furthermore, the qualitative assessment synthesized in this work can serve as a reference material on addressing the areas of improvement of the field and on assessing the capability and potential of the different yeast surface display strategies on the efficient degradation, utilization, and ethanol production from lignocellulosic biomass.
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44
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Kim ES, Kim BS, Kim KY, Woo HM, Lee SM, Um Y. Aerobic and anaerobic cellulose utilization by Paenibacillus sp. CAA11 and enhancement of its cellulolytic ability by expressing a heterologous endoglucanase. J Biotechnol 2018; 268:21-27. [PMID: 29339118 DOI: 10.1016/j.jbiotec.2018.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/09/2018] [Accepted: 01/12/2018] [Indexed: 12/21/2022]
Abstract
For cost-effective lignocellulosic biofuel/chemical production, consolidated bioprocessing (CBP)-enabling microorganisms utilizing cellulose as well as producing biofuel/chemical are required. A novel strain Paenibacillus sp. CAA11 isolated from sediment was found to be not only as a cellulose degrader under both aerobic and strict anaerobic conditions but also as a producer of cellulosic biofuel/chemicals. Paenibacillus sp. CAA11 secreted cellulolytic enzymes by its own secretion system and produced ethanol as well as short-chain organic acids (formic acid, acetic acid, lactic acid) from cellulose. Cellulolytic activity of the strain was significantly enhanced by expressing a heterologous endoglucanase 168Cel5 from Bacillus subtilis under both aerobic and anaerobic conditions. The strain harboring the 168cel5 gene revealed 2-fold bigger halo zone on Congo-red plate and 1.75-fold more aerobic cellulose utilization in liquid medium compared with the negative control. Notably, under anaerobic conditions, the recombinant strain expressing 168Cel5 consumed 1.83-fold more cellulose (5.10 g/L) and produced 5-fold more ethanol (0.65 g/L) along with 5-fold more total acids (1.6 g/L) compared with the control, resulting 2.73-fold higher yields. This result demonstrates the potential of Paenibacillus sp. CAA11 as a suitable aerobic and anaerobic CBP-enabling microbe with cellulolytic production of ethanol and short-chain organic acids.
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Affiliation(s)
- Eun Sook Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Byeong-Soo Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Ki-Yeon Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; Clean Energy and Chemical Engineering, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Han-Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; Green School (Graduate School of Energy and Environment), Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; Clean Energy and Chemical Engineering, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
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45
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Verdorfer T, Bernardi RC, Meinhold A, Ott W, Luthey-Schulten Z, Nash MA, Gaub HE. Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics. J Am Chem Soc 2017; 139:17841-17852. [PMID: 29058444 PMCID: PMC5737924 DOI: 10.1021/jacs.7b07574] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cellulosomes are polyprotein machineries that efficiently degrade cellulosic material. Crucial to their function are scaffolds consisting of highly homologous cohesin domains, which serve a dual role by coordinating a multiplicity of enzymes as well as anchoring the microbe to its substrate. Here we combined two approaches to elucidate the mechanical properties of the main scaffold ScaA of Acetivibrio cellulolyticus. A newly developed parallelized one-pot in vitro transcription-translation and protein pull-down protocol enabled high-throughput atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) measurements of all cohesins from ScaA with a single cantilever, thus promising improved relative force comparability. Albeit very similar in sequence, the hanging cohesins showed considerably lower unfolding forces than the bridging cohesins, which are subjected to force when the microbe is anchored to its substrate. Additionally, all-atom steered molecular dynamics (SMD) simulations on homology models offered insight into the process of cohesin unfolding under force. Based on the differences among the individual force propagation pathways and their associated correlation communities, we designed mutants to tune the mechanical stability of the weakest hanging cohesin. The proposed mutants were tested in a second high-throughput AFM SMFS experiment revealing that in one case a single alanine to glycine point mutation suffices to more than double the mechanical stability. In summary, we have successfully characterized the force induced unfolding behavior of all cohesins from the scaffoldin ScaA, as well as revealed how small changes in sequence can have large effects on force resilience in cohesin domains. Our strategy provides an efficient way to test and improve the mechanical integrity of protein domains in general.
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Affiliation(s)
- Tobias Verdorfer
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Rafael C Bernardi
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aylin Meinhold
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Wolfgang Ott
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Zaida Luthey-Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Michael A Nash
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), 4058 Basel, Switzerland
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
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46
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Chen Q, Yu S, Myung N, Chen W. DNA-guided assembly of a five-component enzyme cascade for enhanced conversion of cellulose to gluconic acid and H 2 O 2. J Biotechnol 2017; 263:30-35. [DOI: 10.1016/j.jbiotec.2017.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/25/2017] [Accepted: 10/09/2017] [Indexed: 01/17/2023]
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47
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Yang CE, Chu IM, Wei YH, Tsai SL. Surface display of synthetic phytochelatins on Saccharomyces cerevisiae for enhanced ethanol production in heavy metal-contaminated substrates. BIORESOURCE TECHNOLOGY 2017; 245:1455-1460. [PMID: 28596072 DOI: 10.1016/j.biortech.2017.05.127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 06/07/2023]
Abstract
The aim of this work was to study the feasibility of surface displaying synthetic phytochelatin (EC) on Saccharomyces cerevisiae to overcome the inhibitory effect of heavy metals on ethanol production. Via the fusion of a gene encoding EC to an α-agglutinin gene, the engineered S. cerevisiae was able to successfully display EC on its surface. This surface engineered yeast strain exhibited an efficient cadmium adsorption capability and a remarkably enhanced cadmium tolerance. Moreover, its ethanol production efficiency was significantly improved as compared to a control strain in the presence of cadmium. Similar results could also be observed in the presence of other metals, such as nickel, lead and copper. Overall, this method allows simultaneous biorefinery and heavy metal removal when using heavy metal-contaminated biomass as raw materials.
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Affiliation(s)
- Chi-En Yang
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - I-Ming Chu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yu-Hong Wei
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan 32003, Taiwan
| | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan.
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48
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Selwal KK, Li YF, Yu Z. Functional display of amylase on yeast surface from Rhizopus oryzae as a novel enzyme delivery method. FOOD BIOTECHNOL 2017. [DOI: 10.1080/08905436.2017.1369098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Krishan K. Selwal
- Department of Biotechnology, DCR University of Science & Technology, Murthal (Sonepat), Haryana, India
- Department of Animal Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Yueh-Fen Li
- Department of Animal Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, Ohio, USA
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49
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Gandini C, Tarraran L, Kalemasi D, Pessione E, Mazzoli R. RecombinantLactococcus lactisfor efficient conversion of cellodextrins into L-lactic acid. Biotechnol Bioeng 2017; 114:2807-2817. [DOI: 10.1002/bit.26400] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/01/2017] [Accepted: 08/07/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Chiara Gandini
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
| | - Loredana Tarraran
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
| | - Denis Kalemasi
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
| | - Enrica Pessione
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
| | - Roberto Mazzoli
- Department of Life Sciences and Systems Biology, Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes; University of Turin; Torino Italy
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50
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Xu Q, Knoshaug EP, Wang W, Alahuhta M, Baker JO, Yang S, Vander Wall T, Decker SR, Himmel ME, Zhang M, Wei H. Expression and secretion of fungal endoglucanase II and chimeric cellobiohydrolase I in the oleaginous yeast Lipomyces starkeyi. Microb Cell Fact 2017; 16:126. [PMID: 28738851 PMCID: PMC5525229 DOI: 10.1186/s12934-017-0742-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/13/2017] [Indexed: 11/29/2022] Open
Abstract
Background Lipomyces starkeyi is one of the leading lipid-producing microorganisms reported to date; its genetic transformation was only recently reported. Our aim is to engineer L. starkeyi to serve in consolidated bioprocessing (CBP) to produce lipid or fatty acid-related biofuels directly from abundant and low-cost lignocellulosic substrates. Results To evaluate L. starkeyi in this role, we first conducted a genome analysis, which revealed the absence of key endo- and exocellulases in this yeast, prompting us to select and screen four signal peptides for their suitability for the overexpression and secretion of cellulase genes. To compensate for the cellulase deficiency, we chose two prominent cellulases, Trichoderma reesei endoglucanase II (EG II) and a chimeric cellobiohydrolase I (TeTrCBH I) formed by fusion of the catalytic domain from Talaromyces emersonii CBH I with the linker peptide and cellulose-binding domain from T. reesei CBH I. The systematically tested signal peptides included three peptides from native L. starkeyi and one from Yarrowia lipolytica. We found that all four signal peptides permitted secretion of active EG II. We also determined that three of these signal peptides worked for expression of the chimeric CBH I; suggesting that our design criteria for selecting these signal peptides was effective. Encouragingly, the Y. lipolytica signal peptide was able to efficiently guide secretion of the chimeric TeTrCBH I protein from L. starkeyi. The purified chimeric TeTrCBH I showed high activity against the cellulose in pretreated corn stover and the purified EG II showed high endocellulase activity measured by the CELLG3 (Megazyme) method. Conclusions Our results suggest that L. starkeyi is capable of expressing and secreting core fungal cellulases. Moreover, the purified EG II and chimeric TeTrCBH I displayed significant and potentially useful enzymatic activities, demonstrating that engineered L. starkeyi has the potential to function as an oleaginous CBP strain for biofuel production. The effectiveness of the tested secretion signals will also benefit future secretion of other heterologous proteins in L. starkeyi and, given the effectiveness of the cross-genus secretion signal, possibly other oleaginous yeasts as well. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0742-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Eric P Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - John O Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Todd Vander Wall
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Stephen R Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Min Zhang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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