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Ding Q, Liu L. Reprogramming cellular metabolism to increase the efficiency of microbial cell factories. Crit Rev Biotechnol 2024; 44:892-909. [PMID: 37380349 DOI: 10.1080/07388551.2023.2208286] [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: 11/17/2022] [Accepted: 04/11/2023] [Indexed: 06/30/2023]
Abstract
Recent studies are increasingly focusing on advanced biotechnological tools, self-adjusting smart microorganisms, and artificial intelligent networks, to engineer microorganisms with various functions. Microbial cell factories are a vital platform for improving the bioproduction of medicines, biofuels, and biomaterials from renewable carbon sources. However, these processes are significantly affected by cellular metabolism, and boosting the efficiency of microbial cell factories remains a challenge. In this review, we present a strategy for reprogramming cellular metabolism to enhance the efficiency of microbial cell factories for chemical biosynthesis, which improves our understanding of microbial physiology and metabolic control. Current methods are mainly focused on synthetic pathways, metabolic resources, and cell performance. This review highlights the potential biotechnological strategy to reprogram cellular metabolism and provide novel guidance for designing more intelligent industrial microbes with broader applications in this growing field.
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Affiliation(s)
- Qiang Ding
- School of Life Sciences, Anhui University, Hefei, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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2
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Yan W, Li X, Zhao D, Xie M, Li T, Qian L, Ye C, Shi T, Wu L, Wang Y. Advanced strategies in high-throughput droplet screening for enzyme engineering. Biosens Bioelectron 2024; 248:115972. [PMID: 38171222 DOI: 10.1016/j.bios.2023.115972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/05/2023] [Accepted: 12/23/2023] [Indexed: 01/05/2024]
Abstract
Enzymes, as biocatalysts, play a cumulatively important role in environmental purification and industrial production of chemicals and pharmaceuticals. However, natural enzymes are limited by their physiological properties in practice, which need to be modified driven by requirements. Screening and isolating certain enzyme variants or ideal industrial strains with high yielding of target product enzymes is one of the main directions of enzyme engineering research. Droplet-based high-throughput screening (DHTS) technology employs massive monodisperse emulsion droplets as microreactors to achieve single strain encapsulation, as well as continuous monitoring for the inside mutant library. It can effectively sort out strains or enzymes with desired characteristics, offering a throughput of 108 events per hour. Much of the early literature focused on screening various engineered strains or designing signalling sorting strategies based on DHTS technology. However, the field of enzyme engineering lacks a comprehensive overview of advanced methods for microfluidic droplets and their cutting-edge developments in generation and manipulation. This review emphasizes the advanced strategies and frontiers of microfluidic droplet generation and manipulation facilitating enzyme engineering development. We also introduce design for various screening signals that cooperate with DHTS and devote to enzyme engineering.
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Affiliation(s)
- Wenxin Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Xiang Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Danshan Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Meng Xie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Ting Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Lu Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China; Ministry of Education Key Laboratory of NSLSCS, Nanjing Normal University, Nanjing 210046, China.
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China.
| | - Lina Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China; Food Laboratory of Zhongyuan, Luohe, 462300, Henan, China.
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China.
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3
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Zhang W, Dong H, Wang X, Zhang L, Chen C, Wang P. Engineered Escherichia coli Consortia Function in a Programmable Pattern for Multiple Enzymatic Biosynthesis. ACS APPLIED MATERIALS & INTERFACES 2023; 15:45886-45894. [PMID: 37738613 DOI: 10.1021/acsami.3c09123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Coordinating microbial consortia to realize complex synthetic pathways is an area of great interest in the rapidly growing field of biomanufacturing. This work presents a programmable method for assembling living cells based on the surface display of affinity groups, enabling whole-cell catalysis with optimized catalytic efficiency through the rational arrangement of cell assemblies and enzymes. In the context of d-phenyllactic acid (d-PLA) synthesis, four enzymes were rationally arranged considering substrate channeling and protein expression levels. The production efficiencies of d-PLA catalyzed by engineered microbial consortia were 1.31- and 2.55-fold higher than those of biofilm and whole-cell catalysts, respectively. Notably, substrate channeling was identified between the coimmobilized rate-limiting enzymes, resulting in a 3.67-fold improvement in catalytic efficiency compared with hybrid catalysts (free enzymes coupled with whole-cell catalysts). The highest yield of d-PLA catalyzed by microbial consortia was 102.85 ± 3.39 mM with 140 mM benzaldehyde as the substrate. This study proposes a novel approach to cell enzyme assembly for coordinating microbial consortia in multiple enzymatic biosynthesis processes.
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Affiliation(s)
- Wenxue Zhang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Hao Dong
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiaoli Wang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Liting Zhang
- Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Chao Chen
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
- Institute for Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Ping Wang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St Paul, Minnesota 55108, United States
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4
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Effect of multimodularity and spatial organization of glycoside hydrolases on catalysis. Essays Biochem 2023; 67:629-638. [PMID: 36866571 DOI: 10.1042/ebc20220167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 03/04/2023]
Abstract
The wide diversity among the carbohydrate-active enzymes (CAZymes) reflects the equally broad versatility in terms of composition and chemicals bonds found in the plant cell wall polymers on which they are active. This diversity is also expressed through the various strategies developed to circumvent the recalcitrance of these substrates to biological degradation. Glycoside hydrolases (GHs) are the most abundant of the CAZymes and are expressed as isolated catalytic modules or in association with carbohydrate-binding module (CBM), acting in synergism within complex arrays of enzymes. This multimodularity can be even more complex. The cellulosome presents a scaffold protein immobilized to the outer membrane of some microorganisms on which enzymes are grafted to prevent their dispersion and increase catalytic synergism. In polysaccharide utilization loci (PUL), GHs are also distributed across the membranes of some bacteria to co-ordinate the deconstruction of polysaccharides and the internalization of metabolizable carbohydrates. Although the study and characterization of these enzymatic activities need to take into account the entirety of this complex organization-in particular because of the dynamics involved in it-technical problems limit the present study to isolated enzymes. However, these enzymatic complexes also have a spatiotemporal organization, whose still neglected aspect must be considered. In the present review, the different levels of multimodularity that can occur in GHs will be reviewed, from its simplest forms to the most complex. In addition, attempts to characterize or study the effect on catalytic activity of the spatial organization within GHs will be addressed.
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Khalili M, Williams CJ, Micallef C, Duarte-Martinez F, Afsar A, Zhang R, Wilson S, Dossi E, Impey SA, Goel S, Aria AI. Nanoindentation Response of 3D Printed PEGDA Hydrogels in a Hydrated Environment. ACS APPLIED POLYMER MATERIALS 2023; 5:1180-1190. [PMID: 36817334 PMCID: PMC9926483 DOI: 10.1021/acsapm.2c01700] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/27/2022] [Indexed: 05/09/2023]
Abstract
Hydrogels are commonly used materials in tissue engineering and organ-on-chip devices. This study investigated the nanomechanical properties of monolithic and multilayered poly(ethylene glycol) diacrylate (PEGDA) hydrogels manufactured using bulk polymerization and layer-by-layer projection lithography processes, respectively. An increase in the number of layers (or reduction in layer thickness) from 1 to 8 and further to 60 results in a reduction in the elastic modulus from 5.53 to 1.69 and further to 0.67 MPa, respectively. It was found that a decrease in the number of layers induces a lower creep index (CIT) in three-dimensional (3D) printed PEGDA hydrogels. This reduction is attributed to mesoscale imperfections that appear as pockets of voids at the interfaces of the multilayered hydrogels attributed to localized regions of unreacted prepolymers, resulting in variations in defect density in the samples examined. An increase in the degree of cross-linking introduced by a higher dosage of ultraviolet (UV) exposure leads to a higher elastic modulus. This implies that the elastic modulus and creep behavior of hydrogels are governed and influenced by the degree of cross-linking and defect density of the layers and interfaces. These findings can guide an optimal manufacturing pathway to obtain the desirable nanomechanical properties in 3D printed PEGDA hydrogels, critical for the performance of living cells and tissues, which can be engineered through control of the fabrication parameters.
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Affiliation(s)
- Mohammad
Hakim Khalili
- Surface
Engineering and Precision Centre, School of Aerospace, Transport and
Manufacturing, Cranfield University, Cranfield MK43 0AL, U.K.
| | - Craig J. Williams
- The
Henry Royce Institute, Department of Materials, The University of Manchester, Manchester M13 9PL, U.K.
| | - Christian Micallef
- Surface
Engineering and Precision Centre, School of Aerospace, Transport and
Manufacturing, Cranfield University, Cranfield MK43 0AL, U.K.
| | - Fabian Duarte-Martinez
- Surface
Engineering and Precision Centre, School of Aerospace, Transport and
Manufacturing, Cranfield University, Cranfield MK43 0AL, U.K.
| | - Ashfaq Afsar
- School
of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K.
- Centre
for Defence Chemistry, Cranfield University, Shrivenham, Swindon SN6 8LA, U.K.
| | - Rujing Zhang
- Sophion
Bioscience A/S, Baltorpvej 154, 2750 Ballerup, Denmark
| | - Sandra Wilson
- Sophion
Bioscience A/S, Baltorpvej 154, 2750 Ballerup, Denmark
| | - Eleftheria Dossi
- Centre
for Defence Chemistry, Cranfield University, Shrivenham, Swindon SN6 8LA, U.K.
| | - Susan A. Impey
- Surface
Engineering and Precision Centre, School of Aerospace, Transport and
Manufacturing, Cranfield University, Cranfield MK43 0AL, U.K.
| | - Saurav Goel
- London South
Bank University, 103
Borough Road, London SE1
0AA, U.K.
- University
of Petroleum and Energy Studies, Dehradun 248007, India
| | - Adrianus Indrat Aria
- Surface
Engineering and Precision Centre, School of Aerospace, Transport and
Manufacturing, Cranfield University, Cranfield MK43 0AL, U.K.
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Dong H, Zhang W, Zhou S, Ying H, Wang P. Rational Design of Artificial Biofilms as Sustainable Supports for Whole-Cell Catalysis Through Integrating Extra- and Intracellular Catalysis. CHEMSUSCHEM 2022; 15:e202200850. [PMID: 35726119 PMCID: PMC9543694 DOI: 10.1002/cssc.202200850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/13/2022] [Indexed: 05/31/2023]
Abstract
Biofilms are promising candidates for sustainable bioprocessing applications. This work presents a rational design of biofilm catalysts by integrating extra- and intracellular catalysis systems with optimized substrate channeling to realize efficient multistep biosynthesis. An assembly of four enzymes in a "three-in-one" structure was achieved by rationally placing the enzymes on curli nanofibers, the cell surface, and inside cells. The catalytic efficiency of the biofilm catalysts was over 2.8 folds higher than that of the control whole-cell catalysis when the substrate benzaldehyde was fed at 100 mm. The highest yield of d-phenyllactic acid catalyzed by biofilm catalysts under optimized conditions was 102.19 mm, also much higher than that of the control catalysis test (52.29 mm). The results demonstrate that engineered biofilms are greatly promising in integrating extra- and intracellular catalysis, illustrating great potentials of rational design in constructing biofilm catalysts as sustainable supports for whole-cell catalysis.
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Affiliation(s)
- Hao Dong
- 1 State Key Laboratory of Bioreactor EngineeringSchool of BiotechnologyEast China University of Science and TechnologyShanghai200237P. R. China
- College of Food Science and EngineeringOcean University of ChinaQingdao266003P. R. China
| | - Wenxue Zhang
- 1 State Key Laboratory of Bioreactor EngineeringSchool of BiotechnologyEast China University of Science and TechnologyShanghai200237P. R. China
| | - Shengmin Zhou
- 1 State Key Laboratory of Bioreactor EngineeringSchool of BiotechnologyEast China University of Science and TechnologyShanghai200237P. R. China
| | - Hanjie Ying
- National Engineering Research Center for BiotechnologyNanjing Tech UniversityNO.30 Puzhu Road(S)NanjingJS 211816P. R. China
| | - Ping Wang
- 1 State Key Laboratory of Bioreactor EngineeringSchool of BiotechnologyEast China University of Science and TechnologyShanghai200237P. R. China
- Department of Bioproducts and Biosystems EngineeringUniversity of MinnesotaSt. PaulMN 55108USA
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Abstract
The market for industrial enzymes has witnessed constant growth, which is currently around 7% a year, projected to reach $10.5 billion in 2024. Lipases are hydrolase enzymes naturally responsible for triglyceride hydrolysis. They are the most expansively used industrial biocatalysts, with wide application in a broad range of industries. However, these biocatalytic processes are usually limited by the low stability of the enzyme, the half-life time, and the processes required to solve these problems are complex and lack application feasibility at the industrial scale. Emerging technologies create new materials for enzyme carriers and sophisticate the well-known immobilization principles to produce more robust, eco-friendlier, and cheaper biocatalysts. Therefore, this review discusses the trending studies and industrial applications of the materials and protocols for lipase immobilization, analyzing their advantages and disadvantages. Finally, it summarizes the current challenges and potential alternatives for lipases at the industrial level.
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Omidvar M, Zdarta J, Sigurdardóttir SB, Pinelo M. Mimicking natural strategies to create multi-environment enzymatic reactors: From natural cell compartments to artificial polyelectrolyte reactors. Biotechnol Adv 2021; 54:107798. [PMID: 34265377 DOI: 10.1016/j.biotechadv.2021.107798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/09/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022]
Abstract
Engineering microenvironments for sequential enzymatic reactions has attracted specific interest within different fields of research as an effective strategy to improve the catalytic performance of enzymes. While in industry most enzymatic reactions occur in a single compartment carrier, living cells are however able to conduct multiple reactions simultaneously within confined sub-compartments, or organelles. Engineering multi-compartments with regulated environments and transformation properties enhances enzyme activity and stability and thus increases the overall yield of final products. In this review, we discuss current and potential methods to fabricate artificial cells for sequential enzymatic reactions, which are inspired by mechanisms and metabolic pathways developed by living cells. We aim to advance the understanding of living cell complexity and its compartmentalization and present solutions to mimic these processes in vitro. Particular attention has been given to layer-by-layer assembly of polyelectrolytes for developing multi-compartments. We hope this review paves the way for the next steps toward engineering of smart artificial multi-compartments with adoptive stimuli-responsive properties, mimicking living cells to improve catalytic properties and efficiency of the enzymes and enhance their stability.
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Affiliation(s)
- Maryam Omidvar
- Process and Systems Engineering Centre, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark
| | - Jakub Zdarta
- Process and Systems Engineering Centre, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark; Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, 60965 Poznan, Poland
| | - Sigyn Björk Sigurdardóttir
- Process and Systems Engineering Centre, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark
| | - Manuel Pinelo
- Process and Systems Engineering Centre, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark.
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