1
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Wang R, Su Y, Yang W, Zhang H, Wang J, Gao W. Enhanced precision and efficiency in metabolic regulation: Compartmentalized metabolic engineering. BIORESOURCE TECHNOLOGY 2024; 402:130786. [PMID: 38703958 DOI: 10.1016/j.biortech.2024.130786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024]
Abstract
Metabolic engineering has witnessed remarkable advancements, enabling successful large-scale, cost-effective and efficient production of numerous compounds. However, the predominant expression of heterologous genes in the cytoplasm poses limitations, such as low substrate concentration, metabolic competition and product toxicity. To overcome these challenges, compartmentalized metabolic engineering allows the spatial separation of metabolic pathways for the efficient and precise production of target compounds. Compartmentalized metabolic engineering and its common strategies are comprehensively described in this study, where various membranous compartments and membraneless compartments have been used for compartmentalization and constructive progress has been made. Additionally, the challenges and future directions are discussed in depth. This review is dedicated to providing compartmentalized, precise and efficient methods for metabolic production, and provides valuable guidance for further development in the field of metabolic engineering.
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Affiliation(s)
- Rubing Wang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Yaowu Su
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Wenqi Yang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Huanyu Zhang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
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2
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Doron L, Kerfeld CA. Bacterial microcompartments as a next-generation metabolic engineering tool: utilizing nature's solution for confining challenging catabolic pathways. Biochem Soc Trans 2024:BST20230229. [PMID: 38813858 DOI: 10.1042/bst20230229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Advancements in synthetic biology have facilitated the incorporation of heterologous metabolic pathways into various bacterial chassis, leading to the synthesis of targeted bioproducts. However, total output from heterologous production pathways can suffer from low flux, enzyme promiscuity, formation of toxic intermediates, or intermediate loss to competing reactions, which ultimately hinder their full potential. The self-assembling, easy-to-modify, protein-based bacterial microcompartments (BMCs) offer a sophisticated way to overcome these obstacles by acting as an autonomous catalytic module decoupled from the cell's regulatory and metabolic networks. More than a decade of fundamental research on various types of BMCs, particularly structural studies of shells and their self-assembly, the recruitment of enzymes to BMC shell scaffolds, and the involvement of ancillary proteins such as transporters, regulators, and activating enzymes in the integration of BMCs into the cell's metabolism, has significantly moved the field forward. These advances have enabled bioengineers to design synthetic multi-enzyme BMCs to promote ethanol or hydrogen production, increase cellular polyphosphate levels, and convert glycerol to propanediol or formate to pyruvate. These pioneering efforts demonstrate the enormous potential of synthetic BMCs to encapsulate non-native multi-enzyme biochemical pathways for the synthesis of high-value products.
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Affiliation(s)
- Lior Doron
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, U.S.A
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3
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Gu S, Bradley-Clarke J, Rose RS, Warren MJ, Pickersgill RW. Enzyme-cargo encapsulation peptides bind between tessellating tiles of the bacterial microcompartment shell. J Biol Chem 2024; 300:107357. [PMID: 38735476 DOI: 10.1016/j.jbc.2024.107357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 04/11/2024] [Accepted: 04/14/2024] [Indexed: 05/14/2024] Open
Abstract
Bacterial microcompartments are prokaryotic organelles comprising encapsulated enzymes within a thin protein shell. They facilitate metabolic processing including propanediol, choline, glycerol, and ethanolamine utilization, and they accelerate carbon fixation in cyanobacteria. Enzymes targeted to the inside of the microcompartment frequently possess a cargo-encapsulation peptide, but the site to which the peptide binds is unclear. We provide evidence that the encapsulation peptides bind to the hydrophobic groove formed between tessellating subunits of the shell proteins. In silico docking studies provide a compelling model of peptide binding to this prominent hydrophobic groove. This result is consistent with the now widely accepted view that the convex side of the shell oligomers faces the lumen of the microcompartment. The binding of the encapsulation peptide to the groove between tessellating shell protein tiles explains why it has been difficult to define the peptide binding site using other methods, provides a mechanism by which encapsulation-peptide bearing enzymes can promote shell assembly, and explains how the presence of cargo affects the size and shape of the bacterial microcompartment. This knowledge may be exploited in engineering microcompartments or disease prevention by hampering cargo encapsulation.
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Affiliation(s)
- Shuang Gu
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, UK
| | - Jack Bradley-Clarke
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, UK
| | - Ruth-Sarah Rose
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Richard W Pickersgill
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, UK.
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4
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Kwon S, Andreas MP, Giessen TW. Pore engineering as a general strategy to improve protein-based enzyme nanoreactor performance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592161. [PMID: 38746127 PMCID: PMC11092584 DOI: 10.1101/2024.05.02.592161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Enzyme nanoreactors are nanoscale compartments consisting of encapsulated enzymes and a selectively permeable barrier. Sequestration and co-localization of enzymes can increase catalytic activity, stability, and longevity, highly desirable features for many biotechnological and biomedical applications of enzyme catalysts. One promising strategy to construct enzyme nanoreactors is to repurpose protein nanocages found in nature. However, protein-based enzyme nanoreactors often exhibit decreased catalytic activity, partially caused by a mismatch of protein shell selectivity and the substrate requirements of encapsulated enzymes. No broadly applicable and modular protein-based nanoreactor platform is currently available. Here, we introduce a pore-engineered universal enzyme nanoreactor platform based on encapsulins - microbial self-assembling protein nanocompartments with programmable and selective enzyme packaging capabilities. We structurally characterize our protein shell designs via cryo-electron microscopy and highlight their polymorphic nature. Through fluorescence polarization assays, we show their improved molecular flux behavior and highlight their expanded substrate range via a number of proof-of-concept enzyme nanoreactor designs. This work lays the foundation for utilizing our encapsulin-based nanoreactor platform for future biotechnological and biomedical applications.
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Affiliation(s)
- Seokmu Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
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5
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Li T, Chang P, Chen W, Shi Z, Xue C, Dykes GF, Huang F, Wang Q, Liu LN. Nanoengineering Carboxysome Shells for Protein Cages with Programmable Cargo Targeting. ACS NANO 2024; 18:7473-7484. [PMID: 38326220 PMCID: PMC10938918 DOI: 10.1021/acsnano.3c11559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Protein nanocages have emerged as promising candidates for enzyme immobilization and cargo delivery in biotechnology and nanotechnology. Carboxysomes are natural proteinaceous organelles in cyanobacteria and proteobacteria and have exhibited great potential in creating versatile nanocages for a wide range of applications given their intrinsic characteristics of self-assembly, cargo encapsulation, permeability, and modularity. However, how to program intact carboxysome shells with specific docking sites for tunable and efficient cargo loading is a key question in the rational design and engineering of carboxysome-based nanostructures. Here, we generate a range of synthetically engineered nanocages with site-directed cargo loading based on an α-carboxysome shell in conjunction with SpyTag/SpyCatcher and Coiled-coil protein coupling systems. The systematic analysis demonstrates that the cargo-docking sites and capacities of the carboxysome shell-based protein nanocages could be precisely modulated by selecting specific anchoring systems and shell protein domains. Our study provides insights into the encapsulation principles of the α-carboxysome and establishes a solid foundation for the bioengineering and manipulation of nanostructures capable of capturing cargos and molecules with exceptional efficiency and programmability, thereby enabling applications in catalysis, delivery, and medicine.
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Affiliation(s)
- Tianpei Li
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Ping Chang
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Weixian Chen
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Zhaoyang Shi
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Chunling Xue
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Gregory F. Dykes
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Fang Huang
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Qiang Wang
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Lu-Ning Liu
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
- MOE
Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science
Center for Deep Ocean Multispheres and Earth System & College
of Marine Life Sciences, Ocean University
of China, Qingdao 266003, China
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6
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Trettel DS, Pacheco SL, Laskie AK, Gonzalez-Esquer CR. Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation. FRONTIERS IN PLANT SCIENCE 2024; 15:1346759. [PMID: 38425792 PMCID: PMC10902431 DOI: 10.3389/fpls.2024.1346759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
The carboxysome is a bacterial microcompartment (BMC) which plays a central role in the cyanobacterial CO2-concentrating mechanism. These proteinaceous structures consist of an outer protein shell that partitions Rubisco and carbonic anhydrase from the rest of the cytosol, thereby providing a favorable microenvironment that enhances carbon fixation. The modular nature of carboxysomal architectures makes them attractive for a variety of biotechnological applications such as carbon capture and utilization. In silico approaches, such as molecular dynamics (MD) simulations, can support future carboxysome redesign efforts by providing new spatio-temporal insights on their structure and function beyond in vivo experimental limitations. However, specific computational studies on carboxysomes are limited. Fortunately, all BMC (including the carboxysome) are highly structurally conserved which allows for practical inferences to be made between classes. Here, we review simulations on BMC architectures which shed light on (1) permeation events through the shell and (2) assembly pathways. These models predict the biophysical properties surrounding the central pore in BMC-H shell subunits, which in turn dictate the efficiency of substrate diffusion. Meanwhile, simulations on BMC assembly demonstrate that assembly pathway is largely dictated kinetically by cargo interactions while final morphology is dependent on shell factors. Overall, these findings are contextualized within the wider experimental BMC literature and framed within the opportunities for carboxysome redesign for biomanufacturing and enhanced carbon fixation.
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Affiliation(s)
- Daniel S. Trettel
- Los Alamos National Laboratory, Bioscience Division, Microbial and Biome Sciences Group, Los Alamos, NM, United States
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7
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Shinde YD, Chowdhury C. Potential utility of bacterial protein nanoreactor for sustainable in-situ biocatalysis in wide range of bioprocess conditions. Enzyme Microb Technol 2024; 173:110354. [PMID: 37988973 DOI: 10.1016/j.enzmictec.2023.110354] [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: 07/19/2023] [Revised: 09/30/2023] [Accepted: 11/04/2023] [Indexed: 11/23/2023]
Abstract
Bacterial microcompartments (MCPs) are proteinaceous organelles that natively encapsulates the enzymes, substrates, and cofactors within a protein shell. They optimize the reaction rates by enriching the substrate in the vicinity of enzymes to increase the yields of the product and mitigate the outward diffusion of the toxic or volatile intermediates. The shell protein subunits of MCP shell are selectively permeable and have specialized pores for the selective inward diffusion of substrates and products release. Given their attributes, MCPs have been recently explored as potential candidates as subcellular nano-bioreactor for the enhanced production of industrially important molecules by exercising pathway encapsulation. In the current study, MCPs have been shown to sustain enzyme activity for extended periods, emphasizing their durability against a range of physical challenges such as temperature, pH and organic solvents. The significance of an intact shell in conferring maximum protection is highlighted by analyzing the differences in enzyme activities inside the intact and broken shell. Moreover, a minimal synthetic shell was designed with recruitment of a heterologous enzyme cargo to demonstrate the improved durability of the enzyme. The encapsulated enzyme was shown to be more stable than its free counterpart under the aforementioned conditions. Bacterial MCP-mediated encapsulation can serve as a potential strategy to shield the enzymes used under extreme conditions by maintaining the internal microenvironment and enhancing their cycle life, thereby opening new means for stabilizing, and reutilizing the enzymes in several bioprocess industries.
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Affiliation(s)
- Yashodhara D Shinde
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, MH 411008, India
| | - Chiranjit Chowdhury
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, MH 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP 201002, India.
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8
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Su Y, Mangus AM, Cordell WT, Pfleger BF. Overcoming barriers to medium-chain fatty alcohol production. Curr Opin Biotechnol 2024; 85:103063. [PMID: 38219523 PMCID: PMC10922944 DOI: 10.1016/j.copbio.2023.103063] [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: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/16/2024]
Abstract
Medium-chain fatty alcohols (mcFaOHs) are aliphatic primary alcohols containing six to twelve carbons that are widely used in materials, pharmaceuticals, and cosmetics. Microbial biosynthesis has been touted as a route to less-abundant chain-length molecules and as a sustainable alternative to current petrochemical processes. Several metabolic engineering strategies for producing mcFaOHs have been demonstrated in the literature, yet processes continue to suffer from poor selectivity and mcFaOH toxicity, leading to reduced titers, rates, and yields of the desired compounds. This opinion examines the current state of microbial mcFaOH biosynthesis, summarizing engineering efforts to tailor selectivity and improve product tolerance by implementing engineering strategies that circumvent or overcome mcFaOH toxicity.
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Affiliation(s)
- Yun Su
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anna M Mangus
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - William T Cordell
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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9
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Zedler JAZ, Schirmacher AM, Russo DA, Hodgson L, Gundersen E, Matthes A, Frank S, Verkade P, Jensen PE. Self-Assembly of Nanofilaments in Cyanobacteria for Protein Co-localization. ACS NANO 2023; 17:25279-25290. [PMID: 38065569 PMCID: PMC10754207 DOI: 10.1021/acsnano.3c08600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 12/27/2023]
Abstract
Cyanobacteria offer great potential as alternative biotechnological hosts due to their photoautotrophic capacities. However, in comparison to established heterotrophic hosts, several key aspects, such as product titers, are still lagging behind. Nanobiotechnology is an emerging field with great potential to improve existing hosts, but so far, it has barely been explored in microbial photosynthetic systems. Here, we report the establishment of large proteinaceous nanofilaments in the unicellular model cyanobacterium Synechocystis sp. PCC 6803 and the fast-growing cyanobacterial strain Synechococcus elongatus UTEX 2973. Transmission electron microscopy and electron tomography demonstrated that expression of pduA*, encoding a modified bacterial microcompartment shell protein, led to the generation of bundles of longitudinally aligned nanofilaments in S. elongatus UTEX 2973 and shorter filamentous structures in Synechocystis sp. PCC 6803. Comparative proteomics showed that PduA* was at least 50 times more abundant than the second most abundant protein in the cell and that nanofilament assembly had only a minor impact on cellular metabolism. Finally, as a proof-of-concept for co-localization with the filaments, we targeted a fluorescent reporter protein, mCitrine, to PduA* by fusion with an encapsulation peptide that natively interacts with PduA. The establishment of nanofilaments in cyanobacterial cells is an important step toward cellular organization of heterologous pathways and the establishment of cyanobacteria as next-generation hosts.
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Affiliation(s)
- Julie A. Z. Zedler
- Synthetic
Biology of Photosynthetic Organisms, Matthias Schleiden Institute
for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Alexandra M. Schirmacher
- Synthetic
Biology of Photosynthetic Organisms, Matthias Schleiden Institute
for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - David A. Russo
- Bioorganic
Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Lorna Hodgson
- School
of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Emil Gundersen
- Department
of Plant and Environmental Sciences, University
of Copenhagen, 1871 Frederiksberg, Denmark
| | - Annemarie Matthes
- Department
of Plant and Environmental Sciences, University
of Copenhagen, 1871 Frederiksberg, Denmark
| | - Stefanie Frank
- Department
of Biochemical Engineering, University College
London, London, WC1E 6BT, United
Kingdom
| | - Paul Verkade
- School
of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Poul Erik Jensen
- Department
of Food Science, University of Copenhagen, 1958 Frederiksberg, Denmark
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10
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Liu N, Dong W, Yang H, Li JH, Chiu TY. Application of artificial scaffold systems in microbial metabolic engineering. Front Bioeng Biotechnol 2023; 11:1328141. [PMID: 38188488 PMCID: PMC10771841 DOI: 10.3389/fbioe.2023.1328141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/12/2023] [Indexed: 01/09/2024] Open
Abstract
In nature, metabolic pathways are often organized into complex structures such as multienzyme complexes, enzyme molecular scaffolds, or reaction microcompartments. These structures help facilitate multi-step metabolic reactions. However, engineered metabolic pathways in microbial cell factories do not possess inherent metabolic regulatory mechanisms, which can result in metabolic imbalance. Taking inspiration from nature, scientists have successfully developed synthetic scaffolds to enhance the performance of engineered metabolic pathways in microbial cell factories. By recruiting enzymes, synthetic scaffolds facilitate the formation of multi-enzyme complexes, leading to the modulation of enzyme spatial distribution, increased enzyme activity, and a reduction in the loss of intermediate products and the toxicity associated with harmful intermediates within cells. In recent years, scaffolds based on proteins, nucleic acids, and various organelles have been developed and employed to facilitate multiple metabolic pathways. Despite varying degrees of success, synthetic scaffolds still encounter numerous challenges. The objective of this review is to provide a comprehensive introduction to these synthetic scaffolds and discuss their latest research advancements and challenges.
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Affiliation(s)
- Nana Liu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| | - Wei Dong
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| | - Huanming Yang
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| | - Jing-Hua Li
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Tsan-Yu Chiu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
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11
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Cheah LC, Liu L, Plan MR, Peng B, Lu Z, Schenk G, Vickers CE, Sainsbury F. Product Profiles of Promiscuous Enzymes Can be Altered by Controlling In Vivo Spatial Organization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303415. [PMID: 37750486 PMCID: PMC10646250 DOI: 10.1002/advs.202303415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/31/2023] [Indexed: 09/27/2023]
Abstract
Enzyme spatial organization is an evolved mechanism for facilitating multi-step biocatalysis and can play an important role in the regulation of promiscuous enzymes. The latter function suggests that artificial spatial organization can be an untapped avenue for controlling the specificity of bioengineered metabolic pathways. A promiscuous terpene synthase (nerolidol synthase) is co-localized and spatially organized with the preceding enzyme (farnesyl diphosphate synthase) in a heterologous production pathway, via translational protein fusion and/or co-encapsulation in a self-assembling protein cage. Spatial organization enhances nerolidol production by ≈11- to ≈62-fold relative to unorganized enzymes. More interestingly, striking differences in the ratio of end products (nerolidol and linalool) are observed with each spatial organization approach. This demonstrates that artificial spatial organization approaches can be harnessed to modulate the product profiles of promiscuous enzymes in engineered pathways in vivo. This extends the application of spatial organization beyond situations where multiple enzymes compete for a single substrate to cases where there is competition among multiple substrates for a single enzyme.
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Affiliation(s)
- Li Chen Cheah
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- Present address:
Australian Centre for Disease Preparedness5 Portarlington RdEast GeelongVIC3219Australia
| | - Lian Liu
- Metabolomics Australia (Queensland Node)The University of QueenslandSt LuciaQLD4072Australia
| | - Manuel R. Plan
- Metabolomics Australia (Queensland Node)The University of QueenslandSt LuciaQLD4072Australia
| | - Bingyin Peng
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
- School of Biological and Environmental ScienceQueensland University of TechnologyBrisbaneQLD4000Australia
| | - Zeyu Lu
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
| | - Gerhard Schenk
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLD4072Australia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
- School of Biological and Environmental ScienceQueensland University of TechnologyBrisbaneQLD4000Australia
- Centre for Cell Factories and BiopolymersGriffith Institute for Drug DiscoveryGriffith UniversityNathanQLD4111Australia
| | - Frank Sainsbury
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- Centre for Cell Factories and BiopolymersGriffith Institute for Drug DiscoveryGriffith UniversityNathanQLD4111Australia
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12
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Quinton AR, McDowell HB, Hoiczyk E. Encapsulins: Nanotechnology's future in a shell. ADVANCES IN APPLIED MICROBIOLOGY 2023; 125:1-48. [PMID: 38783722 DOI: 10.1016/bs.aambs.2023.09.001] [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: 05/25/2024]
Abstract
Encapsulins, virus capsid-like bacterial nanocompartments have emerged as promising tools in medicine, imaging, and material sciences. Recent work has shown that these protein-bound icosahedral 'organelles' possess distinct properties that make them exceptionally usable for nanotechnology applications. A key factor contributing to their appeal is their ability to self-assemble, coupled with their capacity to encapsulate a wide range of cargos. Their genetic manipulability, stability, biocompatibility, and nano-size further enhance their utility, offering outstanding possibilities for practical biotechnology applications. In particular, their amenability to engineering has led to their extensive modification, including the packaging of non-native cargos and the utilization of the shell surface for displaying immunogenic or targeting proteins and peptides. This inherent versatility, combined with the ease of expressing encapsulins in heterologous hosts, promises to provide broad usability. Although mostly not yet commercialized, encapsulins have started to demonstrate their vast potential for biotechnology, from drug delivery to biofuel production and the synthesis of valuable inorganic materials. In this review, we will initially discuss the structure, function and diversity of encapsulins, which form the basis for these emerging applications, before reviewing ongoing practical uses and highlighting promising applications in medicine, engineering and environmental sciences.
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Affiliation(s)
- Amy Ruth Quinton
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Harry Benjamin McDowell
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Egbert Hoiczyk
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom.
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13
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Kumar G, Hazra JP, Sinha S. Disordered regions endow structural flexibility to shell proteins and function towards shell-enzyme interactions in 1,2-propanediol utilization microcompartment. J Biomol Struct Dyn 2023; 41:8891-8901. [PMID: 36318590 DOI: 10.1080/07391102.2022.2138552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/16/2022] [Indexed: 11/07/2022]
Abstract
Intrinsically disordered regions in proteins have been functionally linked to the protein-protein interactions and genesis of several membraneless organelles. Depending on their residual makeup, hydrophobicity or charge distribution they may remain in extended form or may assume certain conformations upon biding to a partner protein or peptide. The present work investigates the distribution and potential roles of disordered regions in the integral proteins of 1,2-propanediol utilization microcompartments. We use bioinformatics tools to identify the probable disordered regions in the shell proteins and enzyme of the 1,2-propanediol utilization microcompartment. Using a combination of computational modelling and biochemical techniques we elucidate the role of disordered terminal regions of a major shell protein and enzyme. Our findings throw light on the importance of disordered regions in the self-assembly, providing flexibility to shell protein and mediating its interaction with a native enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gaurav Kumar
- Chemical Biology Unit, Institute of Nano Science and Technology, Mohali, India
| | - Jagadish Prasad Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Sharmistha Sinha
- Chemical Biology Unit, Institute of Nano Science and Technology, Mohali, India
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14
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Beal DM, Liang M, Brown I, Budge JD, Burrows ER, Howland K, Lee P, Martin S, Morrell A, Nemoto-Smith E, Roobol J, Stanley M, Smales CM, Warren MJ. Modification of bacterial microcompartments with target biomolecules via post-translational SpyTagging. MATERIALS ADVANCES 2023; 4:2963-2970. [PMID: 37465645 PMCID: PMC10350929 DOI: 10.1039/d3ma00071k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/31/2023] [Indexed: 07/20/2023]
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelle-like structures formed within bacteria, often encapsulating enzymes and cellular processes, in particular, allowing toxic intermediates to be shielded from the general cellular environment. Outside of their biological role they are of interest, through surface modification, as potential drug carriers and polyvalent antigen display scaffolds. Here we use a post-translational modification approach, using copper free click chemistry, to attach a SpyTag to a target protein molecule for attachment to a specific SpyCatcher modified BMC shell protein. We demonstrate that a post-translationally SpyTagged material can react with a SpyCatcher modified BMC and show its presence on the surface of BMCs, enabling future investigation of these structures as polyvalent antigen display scaffolds for vaccine development. This post-translational 'click' methodology overcomes the necessity to genetically encode the SpyTag, avoids any potential reduction in expression yield and expands the scope of SpyTag/SpyCatcher vaccine scaffolds to form peptide epitope vaccines and small molecule delivery agents.
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Affiliation(s)
- David M Beal
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Mingzhi Liang
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Ian Brown
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - James D Budge
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | | | - Kevin Howland
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Phoebe Lee
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | | | - Andrew Morrell
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | | | - Joanne Roobol
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Maria Stanley
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - C Mark Smales
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co Dublin A94 X099 Ireland
| | - Martin J Warren
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
- Quadram Institute Bioscience Norwich UK
- Norwich Medical School, University of East Anglia Norwich UK
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15
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Abrahamson CH, Palmero BJ, Kennedy NW, Tullman-Ercek D. Theoretical and Practical Aspects of Multienzyme Organization and Encapsulation. Annu Rev Biophys 2023; 52:553-572. [PMID: 36854212 DOI: 10.1146/annurev-biophys-092222-020832] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The advent of biotechnology has enabled metabolic engineers to assemble heterologous pathways in cells to produce a variety of products of industrial relevance, often in a sustainable way. However, many pathways face challenges of low product yield. These pathways often suffer from issues that are difficult to optimize, such as low pathway flux and off-target pathway consumption of intermediates. These issues are exacerbated by the need to balance pathway flux with the health of the cell, particularly when a toxic intermediate builds up. Nature faces similar challenges and has evolved spatial organization strategies to increase metabolic pathway flux and efficiency. Inspired by these strategies, bioengineers have developed clever strategies to mimic spatial organization in nature. This review explores the use of spatial organization strategies, including protein scaffolding and protein encapsulation inside of proteinaceous shells, toward overcoming bottlenecks in metabolic engineering efforts.
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Affiliation(s)
- Charlotte H Abrahamson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA;
| | - Brett J Palmero
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois, USA
| | - Nolan W Kennedy
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA;
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
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16
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Wang R, Liu X, Lv B, Sun W, Li C. Designing Intracellular Compartments for Efficient Engineered Microbial Cell Factories. ACS Synth Biol 2023; 12:1378-1395. [PMID: 37083286 DOI: 10.1021/acssynbio.2c00671] [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] [Indexed: 04/22/2023]
Abstract
With the rapid development of synthetic biology, various kinds of microbial cell factories (MCFs) have been successfully constructed to produce high-value-added compounds. However, the complexity of metabolic regulation and pathway crosstalk always cause issues such as intermediate metabolite accumulation, byproduct generation, and metabolic burden in MCFs, resulting in low efficiencies and low yields of industrial biomanufacturing. Such issues could be solved by spatially rearranging the pathways using intracellular compartments. In this review, design strategies are summarized and discussed based on the types and characteristics of natural and artificial subcellular compartments. This review systematically presents information for the construction of efficient MCFs with intracellular compartments in terms of four aspects of design strategy goals: (1) improving local reactant concentration; (2) intercepting and isolating competing pathways; (3) providing specific reaction substances and environments; and (4) storing and accumulating products.
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Affiliation(s)
- Ruwen Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Xin Liu
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
| | - Bo Lv
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Wentao Sun
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
- Center for Synthetic and System Biology, Tsinghua University, Beijing, 100084, PR China
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17
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Liu M, Wang Y, Jiang H, Han Y, Xia J. Synthetic Multienzyme Assemblies for Natural Product Biosynthesis. Chembiochem 2023; 24:e202200518. [PMID: 36625563 DOI: 10.1002/cbic.202200518] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
In nature, enzymes that catalyze sequential reactions are often assembled as clusters or complexes. The formation of multienzyme complexes, or metabolons, brings the enzyme active sites into proximity to promote intermediate transfer, decrease intermediate leakage, and streamline the metabolic flux towards the desired products. We and others have developed synthetic versions of metabolons through various strategies to enhance the catalytic rates for synthesizing valuable chemicals inside microbes. Synthetic multienzyme complexes range from static enzyme nanostructures to dynamic enzyme coacervates. Enzyme complexation optimizes the metabolic fluxes inside microbes, increases the product titer, and supplies the field with high-yield microbe strains that are amenable to large-scale fermentation. Enzyme complexes constructed inside microbial cells can be separated as independent entities and catalyze biosynthetic reactions ex vivo; such a feature gains these complexes another name, "synthetic organelles" - new subcellular entities with independent structures and functions. Still, the field is seeking new strategies to better balance dynamicity and confinement and to achieve finer control of local compartmentalization in the cells, as the natural multienzyme complexes do. Industrial applications of synthetic multienzyme complexes for the large-scale production of valuable chemicals are yet to be realized. This review focuses on synthetic multienzyme complexes that are constructed and function inside microbial cells.
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Affiliation(s)
- Min Liu
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yue Wang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hao Jiang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yongxu Han
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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18
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An B, Wang Y, Huang Y, Wang X, Liu Y, Xun D, Church GM, Dai Z, Yi X, Tang TC, Zhong C. Engineered Living Materials For Sustainability. Chem Rev 2023; 123:2349-2419. [PMID: 36512650 DOI: 10.1021/acs.chemrev.2c00512] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent advances in synthetic biology and materials science have given rise to a new form of materials, namely engineered living materials (ELMs), which are composed of living matter or cell communities embedded in self-regenerating matrices of their own or artificial scaffolds. Like natural materials such as bone, wood, and skin, ELMs, which possess the functional capabilities of living organisms, can grow, self-organize, and self-repair when needed. They also spontaneously perform programmed biological functions upon sensing external cues. Currently, ELMs show promise for green energy production, bioremediation, disease treatment, and fabricating advanced smart materials. This review first introduces the dynamic features of natural living systems and their potential for developing novel materials. We then summarize the recent research progress on living materials and emerging design strategies from both synthetic biology and materials science perspectives. Finally, we discuss the positive impacts of living materials on promoting sustainability and key future research directions.
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Affiliation(s)
- Bolin An
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yanyi Wang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuanyuan Huang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xinyu Wang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuzhu Liu
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dongmin Xun
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - George M Church
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, Massachusetts United States.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston 02115, Massachusetts United States
| | - Zhuojun Dai
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiao Yi
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tzu-Chieh Tang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, Massachusetts United States.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston 02115, Massachusetts United States
| | - Chao Zhong
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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19
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Kim GB, Choi SY, Cho IJ, Ahn DH, Lee SY. Metabolic engineering for sustainability and health. Trends Biotechnol 2023; 41:425-451. [PMID: 36635195 DOI: 10.1016/j.tibtech.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023]
Abstract
Bio-based production of chemicals and materials has attracted much attention due to the urgent need to establish sustainability and enhance human health. Metabolic engineering (ME) allows purposeful modification of cellular metabolic, regulatory, and signaling networks to achieve enhanced production of desired chemicals and degradation of environmentally harmful chemicals. ME has significantly progressed over the past 30 years through further integration of the strategies of synthetic biology, systems biology, evolutionary engineering, and data science aided by artificial intelligence. Here we review the field of ME from its emergence to the current state-of-the-art, highlighting its contribution to sustainable production of chemicals, health, and the environment through representative examples. Future challenges of ME and perspectives are also discussed.
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Affiliation(s)
- Gi Bae Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - In Jin Cho
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Da-Hee Ahn
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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20
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Trettel DS, Winkler WC. In Vitro Analysis of Bacterial Microcompartments and Shell Protein Superstructures by Confocal Microscopy. Microbiol Spectr 2023; 11:e0335722. [PMID: 36786617 PMCID: PMC10100840 DOI: 10.1128/spectrum.03357-22] [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: 08/23/2022] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
The shell proteins that comprise bacterial microcompartments (BMCs) can self-assemble into an array of superstructures such as nanotubes, flat sheets, and icosahedra. The physical characterization of BMCs and these superstructures typically relies on electron microscopy, which decouples samples from their solution context. We hypothesize that an investigation of fluorescently tagged BMCs and shell protein superstructures in vitro using high-resolution confocal microscopy will lead to new insights into the solution behavior of these entities. We find that confocal imaging is able to capture nanotubes and sheets previously reported by transmission electron microscopy (TEM). Using a combination of fluorescent tags, we present qualitative evidence that these structures intermix with one another in a hetero- and homotypic fashion. Complete BMCs are also able to accomplish intermixing as evidenced by colocalization data. Finally, a simple colocalization experiment suggests that fluorescently modified encapsulation peptides (EPs) may prefer certain shell protein binding partners. Together, these data demonstrate that high-resolution confocal microscopy is a powerful tool for investigating microcompartment-related structures in vitro, particularly for colocalization analyses. These results also support the notion that BMCs may intermix protein components, presumably from the outer shell. IMPORTANCE Microcompartments are large, organelle-like structures that help bacteria catabolize targeted metabolites while also protecting the cytosol against highly reactive metabolic intermediates. Their protein shell self-assembles into a polyhedral structure of approximately 100 to 200 nm in diameter. Inside the shell are thousands of copies of cargo enzymes, which are responsible for a specific metabolic pathway. While different approaches have revealed high-resolution structures of individual microcompartment proteins, it is less clear how these factors self-assemble to form the full native structure. In this study, we show that laser scanning confocal microscopy can be used to study microcompartment proteins. We find that this approach allows researchers to investigate the interactions and potential exchange of shell protein subunits in solution. From this, we conclude that confocal microscopy offers advantages for studying the in vitro structures of other microcompartments as well as carboxysomes and other bacterial organelles.
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Affiliation(s)
- Daniel S. Trettel
- Department of Chemistry and Biochemistry, The University of Maryland, College Park, College Park, Maryland, USA
| | - Wade C. Winkler
- Department of Chemistry and Biochemistry, The University of Maryland, College Park, College Park, Maryland, USA
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, College Park, Maryland, USA
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21
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Kwon S, Giessen TW. Engineered Protein Nanocages for Concurrent RNA and Protein Packaging In Vivo. ACS Synth Biol 2022; 11:3504-3515. [PMID: 36170610 PMCID: PMC9944510 DOI: 10.1021/acssynbio.2c00391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Protein nanocages have emerged as an important engineering platform for biotechnological and biomedical applications. Among naturally occurring protein cages, encapsulin nanocompartments have recently gained prominence due to their favorable physico-chemical properties, ease of shell modification, and highly efficient and selective intrinsic protein packaging capabilities. Here, we expand encapsulin function by designing and characterizing encapsulins for concurrent RNA and protein encapsulation in vivo. Our strategy is based on modifying encapsulin shells with nucleic acid-binding peptides without disrupting the native protein packaging mechanism. We show that our engineered encapsulins reliably self-assemble in vivo, are capable of efficient size-selective in vivo RNA packaging, can simultaneously load multiple functional RNAs, and can be used for concurrent in vivo packaging of RNA and protein. Our engineered encapsulation platform has potential for codelivery of therapeutic RNAs and proteins to elicit synergistic effects and as a modular tool for other biotechnological applications.
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Affiliation(s)
- Seokmu Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tobias W. Giessen
- Department of Biological Chemistry and Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
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22
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Raba DA, Kerfeld CA. The potential of bacterial microcompartment architectures for phytonanotechnology. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:700-710. [PMID: 35855583 DOI: 10.1111/1758-2229.13104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
The application of nanotechnology to plants, termed phytonanotechnology, has the potential to revolutionize plant research and agricultural production. Advancements in phytonanotechnology will allow for the time-controlled and target-specific release of bioactive compounds and agrochemicals to alter and optimize conventional plant production systems. A diverse range of engineered nanoparticles with unique physiochemical properties is currently being investigated to determine their suitability for plants. Improvements in crop yield, disease resistance and nutrient and pesticide management are all possible using designed nanocarriers. However, despite these prospective benefits, research to thoroughly understand the precise activity, localization and potential phytotoxicity of these nanoparticles within plant systems is required. Protein-based bacterial microcompartment shell proteins that self-assemble into spherical shells, nanotubes and sheets could be of immense value for phytonanotechnology due to their ease of manipulation, multifunctionality, rapid and efficient producibility and biodegradability. In this review, we explore bacterial microcompartment-based architectures within the scope of phytonanotechnology.
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Affiliation(s)
- Daniel A Raba
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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23
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Otoničar J, Hostnik M, Grundner M, Kostanjšek R, Gredar T, Garvas M, Arsov Z, Podlesek Z, Gostinčar C, Jakše J, Busby SJW, Butala M. A method for targeting a specified segment of DNA to a bacterial microorganelle. Nucleic Acids Res 2022; 50:e113. [PMID: 36029110 DOI: 10.1093/nar/gkac714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/28/2022] [Accepted: 08/09/2022] [Indexed: 11/14/2022] Open
Abstract
Encapsulation of a selected DNA molecule in a cell has important implications for bionanotechnology. Non-viral proteins that can be used as nucleic acid containers include proteinaceous subcellular bacterial microcompartments (MCPs) that self-assemble into a selectively permeable protein shell containing an enzymatic core. Here, we adapted a propanediol utilization (Pdu) MCP into a synthetic protein cage to package a specified DNA segment in vivo, thereby enabling subsequent affinity purification. To this end, we engineered the LacI transcription repressor to be routed, together with target DNA, into the lumen of a Strep-tagged Pdu shell. Sequencing of extracted DNA from the affinity-isolated MCPs shows that our strategy results in packaging of a DNA segment carrying multiple LacI binding sites, but not the flanking regions. Furthermore, we used LacI to drive the encapsulation of a DNA segment containing operators for LacI and for a second transcription factor.
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Affiliation(s)
- Jan Otoničar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maja Hostnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maja Grundner
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Rok Kostanjšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tajda Gredar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maja Garvas
- Jožef Stefan Institute, Condensed Matter Physics Department, 1000 Ljubljana, Slovenia
| | - Zoran Arsov
- Jožef Stefan Institute, Condensed Matter Physics Department, 1000 Ljubljana, Slovenia
| | - Zdravko Podlesek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Stephen J W Busby
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
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24
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Linking the Salmonella enterica 1,2-Propanediol Utilization Bacterial Microcompartment Shell to the Enzymatic Core via the Shell Protein PduB. J Bacteriol 2022; 204:e0057621. [PMID: 35575582 DOI: 10.1128/jb.00576-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Bacterial microcompartments (MCPs) are protein-based organelles that house the enzymatic machinery for metabolism of niche carbon sources, allowing enteric pathogens to outcompete native microbiota during host colonization. While much progress has been made toward understanding MCP biogenesis, questions still remain regarding the mechanism by which core MCP enzymes are enveloped within the MCP protein shell. Here, we explore the hypothesis that the shell protein PduB is responsible for linking the shell of the 1,2-propanediol utilization (Pdu) MCP from Salmonella enterica serovar Typhimurium LT2 to its enzymatic core. Using fluorescent reporters, we demonstrate that all members of the Pdu enzymatic core are encapsulated in Pdu MCPs. We also demonstrate that PduB is critical for linking the entire Pdu enzyme core to the MCP shell. Using MCP purifications, transmission electron microscopy, and fluorescence microscopy, we find that shell assembly can be decoupled from the enzymatic core, as apparently empty MCPs are formed in Salmonella strains lacking PduB. Mutagenesis studies reveal that PduB is incorporated into the Pdu MCP shell via a conserved, lysine-mediated hydrogen bonding mechanism. Finally, growth assays and system-level pathway modeling reveal that unencapsulated pathway performance is strongly impacted by enzyme concentration, highlighting the importance of minimizing polar effects when conducting these functional assays. Together, these results provide insight into the mechanism of enzyme encapsulation within Pdu MCPs and demonstrate that the process of enzyme encapsulation and shell assembly are separate processes in this system, a finding that will aid future efforts to understand MCP biogenesis. IMPORTANCE MCPs are unique, genetically encoded organelles used by many bacteria to survive in resource-limited environments. There is significant interest in understanding the biogenesis and function of these organelles, both as potential antibiotic targets in enteric pathogens and also as useful tools for overcoming metabolic engineering bottlenecks. However, the mechanism by which these organelles are formed natively is still not completely understood. Here, we provide evidence of a potential mechanism in S. enterica by which a single protein, PduB, links the MCP shell and metabolic core. This finding is critical for those seeking to disrupt MCPs during pathogenic infections or for those seeking to harness MCPs as nanobioreactors in industrial settings.
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Edwardson TGW, Levasseur MD, Tetter S, Steinauer A, Hori M, Hilvert D. Protein Cages: From Fundamentals to Advanced Applications. Chem Rev 2022; 122:9145-9197. [PMID: 35394752 DOI: 10.1021/acs.chemrev.1c00877] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.
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Affiliation(s)
| | | | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mao Hori
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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26
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Toward a glycyl radical enzyme containing synthetic bacterial microcompartment to produce pyruvate from formate and acetate. Proc Natl Acad Sci U S A 2022; 119:2116871119. [PMID: 35193962 PMCID: PMC8872734 DOI: 10.1073/pnas.2116871119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 12/15/2022] Open
Abstract
The enormous complexity of metabolic pathways, in both their regulation and propensity for metabolite cross-talk, represents a major obstacle for metabolic engineering. Self-assembling, catalytically programmable and genetically transferable bacterial microcompartments (BMCs) offer solutions to decrease this complexity through compartmentalization of enzymes within a selectively permeable protein shell. Synthetic BMCs can operate as autonomous metabolic modules decoupled from the cell’s regulatory network, only interfacing with the cell’s metabolism via the highly engineerable proteinaceous shell. Here, we build a synthetic, modular, multienzyme BMC. It functions not only as a proof-of-concept for next-generation metabolic engineering, but also provides the foundation for subsequent tuning, with the goal to create a microanaerobic environment protecting an oxygen-sensitive reaction in aerobic growth conditions that could be deployed. Formate has great potential to function as a feedstock for biorefineries because it can be sustainably produced by a variety of processes that don’t compete with agricultural production. However, naturally formatotrophic organisms are unsuitable for large-scale cultivation, difficult to engineer, or have inefficient native formate assimilation pathways. Thus, metabolic engineering needs to be developed for model industrial organisms to enable efficient formatotrophic growth. Here, we build a prototype synthetic formate utilizing bacterial microcompartment (sFUT) encapsulating the oxygen-sensitive glycyl radical enzyme pyruvate formate lyase and a phosphate acyltransferase to convert formate and acetyl-phosphate into the central biosynthetic intermediate pyruvate. This metabolic module offers a defined environment with a private cofactor coenzyme A that can cycle efficiently between the encapsulated enzymes. To facilitate initial design-build-test-refine cycles to construct an active metabolic core, we used a “wiffleball” architecture, defined as an icosahedral bacterial microcompartment (BMC) shell with unoccupied pentameric vertices to freely permit substrate and product exchange. The resulting sFUT prototype wiffleball is an active multi enzyme synthetic BMC functioning as platform technology.
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27
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Trettel DS, Resager W, Ueberheide BM, Jenkins CC, Winkler WC. Chemical probing provides insight into the native assembly state of a bacterial microcompartment. Structure 2022; 30:537-550.e5. [PMID: 35216657 PMCID: PMC8995372 DOI: 10.1016/j.str.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/08/2021] [Accepted: 01/28/2022] [Indexed: 11/28/2022]
Abstract
Bacterial microcompartments (BMCs) are widespread in bacteria and are used for a variety of metabolic purposes, including catabolism of host metabolites. A suite of proteins self-assembles into the shell and cargo layers of BMCs. However, the native assembly state of these large complexes remains to be elucidated. Herein, chemical probes were used to observe structural features of a native BMC. While the exterior could be demarcated with fluorophores, the interior was unexpectedly permeable, suggesting that the shell layer may be more dynamic than previously thought. This allowed access to cross-linking chemical probes, which were analyzed to uncover the protein interactome. These cross-links revealed a complex multivalent network among cargo proteins that contained encapsulation peptides and demonstrated that the shell layer follows discrete rules in its assembly. These results are consistent overall with a model in which biomolecular condensation drives interactions of cargo proteins before envelopment by shell layer proteins.
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Affiliation(s)
- Daniel S Trettel
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - William Resager
- New York University Grossman School of Health, NYU Langone Health, New York, NY 10016, USA
| | - Beatrix M Ueberheide
- New York University Grossman School of Health, NYU Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neurology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Conor C Jenkins
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Wade C Winkler
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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28
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Cheah LC, Stark T, Adamson LSR, Abidin RS, Lau YH, Sainsbury F, Vickers CE. Artificial Self-assembling Nanocompartment for Organizing Metabolic Pathways in Yeast. ACS Synth Biol 2021; 10:3251-3263. [PMID: 34591448 PMCID: PMC8689640 DOI: 10.1021/acssynbio.1c00045] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metabolic pathways are commonly organized by sequestration into discrete cellular compartments. Compartments prevent unfavorable interactions with other pathways and provide local environments conducive to the activity of encapsulated enzymes. Such compartments are also useful synthetic biology tools for examining enzyme/pathway behavior and for metabolic engineering. Here, we expand the intracellular compartmentalization toolbox for budding yeast (Saccharomyces cerevisiae) with Murine polyomavirus virus-like particles (MPyV VLPs). The MPyV system has two components: VP1 which self-assembles into the compartment shell and a short anchor, VP2C, which mediates cargo protein encapsulation via binding to the inner surface of the VP1 shell. Destabilized green fluorescent protein (GFP) fused to VP2C was specifically sorted into VLPs and thereby protected from host-mediated degradation. An engineered VP1 variant displayed improved cargo capture properties and differential subcellular localization compared to wild-type VP1. To demonstrate their ability to function as a metabolic compartment, MPyV VLPs were used to encapsulate myo-inositol oxygenase (MIOX), an unstable and rate-limiting enzyme in d-glucaric acid biosynthesis. Strains with encapsulated MIOX produced ∼20% more d-glucaric acid compared to controls expressing "free" MIOX─despite accumulating dramatically less expressed protein─and also grew to higher cell densities. This is the first demonstration in yeast of an artificial biocatalytic compartment that can participate in a metabolic pathway and establishes the MPyV platform as a promising synthetic biology tool for yeast engineering.
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Affiliation(s)
- Li Chen Cheah
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, Queensland 4102, Australia
| | - Terra Stark
- Metabolomics Australia (Queensland Node), The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lachlan S. R. Adamson
- School of Chemistry, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Rufika S. Abidin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Frank Sainsbury
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, Queensland 4102, Australia
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, Queensland 4102, Australia
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane City, Queensland 4000, Australia
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29
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Burrichter AG, Dörr S, Bergmann P, Haiß S, Keller A, Fournier C, Franchini P, Isono E, Schleheck D. Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia. BMC Microbiol 2021; 21:340. [PMID: 34903181 PMCID: PMC8667426 DOI: 10.1186/s12866-021-02386-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/08/2021] [Indexed: 11/15/2022] Open
Abstract
Background Bilophila wadsworthia, a strictly anaerobic, sulfite-reducing bacterium and common member of the human gut microbiota, has been associated with diseases such as appendicitis and colitis. It is specialized on organosulfonate respiration for energy conservation, i.e., utilization of dietary and host-derived organosulfonates, such as taurine (2-aminoethansulfonate), as sulfite donors for sulfite respiration, producing hydrogen sulfide (H2S), an important intestinal metabolite that may have beneficial as well as detrimental effects on the colonic environment. Its taurine desulfonation pathway involves the glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslAB), which cleaves isethionate (2-hydroxyethanesulfonate) into acetaldehyde and sulfite. Results We demonstrate that taurine metabolism in B. wadsworthia 3.1.6 involves bacterial microcompartments (BMCs). First, we confirmed taurine-inducible production of BMCs by proteomic, transcriptomic and ultra-thin sectioning and electron-microscopical analyses. Then, we isolated BMCs from taurine-grown cells by density-gradient ultracentrifugation and analyzed their composition by proteomics as well as by enzyme assays, which suggested that the GRE IslAB and acetaldehyde dehydrogenase are located inside of the BMCs. Finally, we are discussing the recycling of cofactors in the IslAB-BMCs and a potential shuttling of electrons across the BMC shell by a potential iron-sulfur (FeS) cluster-containing shell protein identified by sequence analysis. Conclusions We characterized a novel subclass of BMCs and broadened the spectrum of reactions known to take place enclosed in BMCs, which is of biotechnological interest. We also provided more details on the energy metabolism of the opportunistic pathobiont B. wadsworthia and on microbial H2S production in the human gut. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02386-w.
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Affiliation(s)
- Anna G Burrichter
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany. .,Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany.
| | - Stefanie Dörr
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paavo Bergmann
- Electron Microscopy Centre, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Sebastian Haiß
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Anja Keller
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | | | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Erika Isono
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
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30
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Tan YQ, Ali S, Xue B, Teo WZ, Ling LH, Go MK, Lv H, Robinson RC, Narita A, Yew WS. Structure of a Minimal α-Carboxysome-Derived Shell and Its Utility in Enzyme Stabilization. Biomacromolecules 2021; 22:4095-4109. [PMID: 34384019 DOI: 10.1021/acs.biomac.1c00533] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bacterial microcompartments are proteinaceous shells that encase specialized metabolic processes in bacteria. Recent advances in simplification of these intricate shells have encouraged bioengineering efforts. Here, we construct minimal shells derived from the Halothiobacillus neapolitanus α-carboxysome, which we term Cso-shell. Using cryogenic electron microscopy, the atomic-level structures of two shell forms were obtained, reinforcing notions of evolutionarily conserved features in bacterial microcompartment shell architecture. Encapsulation peptide sequences that facilitate loading of heterologous protein cargo within the shells were identified. We further provide a first demonstration in utilizing minimal bacterial microcompartment-derived shells for hosting heterologous enzymes. Cso-shells were found to stabilize enzymatic activities against heat shock, presence of methanol co-solvent, consecutive freeze-thawing, and alkaline environments. This study yields insights into α-carboxysome assembly and advances the utility of synthetic bacterial microcompartments as nanoreactors capable of stabilizing enzymes with varied properties and reaction chemistries.
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Affiliation(s)
- Yong Quan Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Graduate School for Integrative Sciences and Engineering, NUS, Singapore 119077
| | - Samson Ali
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Research Institute for Interdisciplinary Science (RIIS), Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Bo Xue
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Wei Zhe Teo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Lay Hiang Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Graduate School for Integrative Sciences and Engineering, NUS, Singapore 119077
| | - Maybelle Kho Go
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Hong Lv
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, People's Republic of China.,State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200438, People's Republic of China
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Akihiro Narita
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Graduate School for Integrative Sciences and Engineering, NUS, Singapore 119077.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
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31
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Montaño López J, Duran L, Avalos JL. Physiological limitations and opportunities in microbial metabolic engineering. Nat Rev Microbiol 2021; 20:35-48. [PMID: 34341566 DOI: 10.1038/s41579-021-00600-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2021] [Indexed: 11/10/2022]
Abstract
Metabolic engineering can have a pivotal role in increasing the environmental sustainability of the transportation and chemical manufacturing sectors. The field has already developed engineered microorganisms that are currently being used in industrial-scale processes. However, it is often challenging to achieve the titres, yields and productivities required for commercial viability. The efficiency of microbial chemical production is usually dependent on the physiological traits of the host organism, which may either impose limitations on engineered biosynthetic pathways or, conversely, boost their performance. In this Review, we discuss different aspects of microbial physiology that often create obstacles for metabolic engineering, and present solutions to overcome them. We also describe various instances in which natural or engineered physiological traits in host organisms have been harnessed to benefit engineered metabolic pathways for chemical production.
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Affiliation(s)
- José Montaño López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Lisset Duran
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA. .,Department of Molecular Biology, Princeton University, Princeton, NJ, USA. .,Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, USA. .,Princeton Environmental Institute, Princeton University, Princeton, NJ, USA.
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32
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Kirst H, Kerfeld CA. Clues to the function of bacterial microcompartments from ancillary genes. Biochem Soc Trans 2021; 49:1085-1098. [PMID: 34196367 PMCID: PMC8517908 DOI: 10.1042/bst20200632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 01/14/2023]
Abstract
Bacterial microcompartments (BMCs) are prokaryotic organelles. Their bounding membrane is a selectively permeable protein shell, encapsulating enzymes of specialized metabolic pathways. While the function of a BMC is dictated by the encapsulated enzymes which vary with the type of the BMC, the shell is formed by conserved protein building blocks. The genes necessary to form a BMC are typically organized in a locus; they encode the shell proteins, encapsulated enzymes as well as ancillary proteins that integrate the BMC function into the cell's metabolism. Among these are transcriptional regulators which usually found at the beginning or end of a locus, and transmembrane proteins that presumably function to conduct the BMC substrate into the cell. Here, we describe the types of transcriptional regulators and permeases found in association with BMC loci, using a recently collected data set of more than 7000 BMC loci distributed over 45 bacterial phyla, including newly discovered BMC loci. We summarize the known BMC regulation mechanisms, and highlight how much remains to be uncovered. We also show how analysis of these ancillary proteins can inform hypotheses about BMC function; by examining the ligand-binding domain of the regulator and the transporter, we propose that nucleotides are the likely substrate for an enigmatic uncharacterized BMC of unknown function.
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Affiliation(s)
- Henning Kirst
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, U.S.A
| | - Cheryl A Kerfeld
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, U.S.A
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, U.S.A
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, U.S.A
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33
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Kumar G, Sinha S. Biophysical approaches to understand and re-purpose bacterial microcompartments. Curr Opin Microbiol 2021; 63:43-51. [PMID: 34166983 DOI: 10.1016/j.mib.2021.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/15/2021] [Accepted: 05/17/2021] [Indexed: 11/30/2022]
Abstract
Bacterial microcompartments represent a modular class of prokaryotic organelles associated with metabolic processes. They harbor a congregation of enzymes that work in cascade within a small, confined volume. These sophisticated nano-engineered crafts of nature offer a tempting paradigm for the fabrication of biosynthetic nanoreactors. Repurposing bacterial microcompartments to develop nanostructures with desired functions requires a careful manipulation in their structural makeup and composition. This calls for a comprehensive understanding of all the interactions of the physical components which frame such molecular architectures. Over recent years, several biophysical techniques have been essential in illuminating the role played by bacterial microcompartments within cells, and have revealed crucial details regarding the morphology, physical properties and functions of their constituent proteins. This has promoted contemplation of ideas for engineering microcompartments inspired biomaterials with novel features and functions.
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Affiliation(s)
- Gaurav Kumar
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector-81, Mohali (SAS Nagar), Knowledge City, Punjab 140306, India
| | - Sharmistha Sinha
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector-81, Mohali (SAS Nagar), Knowledge City, Punjab 140306, India.
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34
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Kennedy NW, Mills CE, Nichols TM, Abrahamson CH, Tullman-Ercek D. Bacterial microcompartments: tiny organelles with big potential. Curr Opin Microbiol 2021; 63:36-42. [PMID: 34126434 DOI: 10.1016/j.mib.2021.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/13/2021] [Accepted: 05/17/2021] [Indexed: 11/28/2022]
Abstract
Organization of metabolic processes within the space of a cell is critical for the survival of many organisms. In bacteria, spatial organization is achieved via proteinaceous organelles called bacterial microcompartments, which encapsulate pathway enzymes, substrates, and co-factors to drive the safe and efficient metabolism of niche carbon sources. Microcompartments are self-assembled from shell proteins that encapsulate a core comprising various enzymes. This review discusses how recent advances in understanding microcompartment structure and assembly have informed engineering efforts to repurpose compartments and compartment-based structures for non-native functions. These advances, both in understanding of the native structure and function of compartments, as well as in the engineering of new functions, will pave the way for the use of these structures in bacterial cell factories.
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Affiliation(s)
- Nolan W Kennedy
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, 2205 Tech Drive, 2-100 Hogan Hall, Evanston, IL, 60208, USA
| | - Carolyn E Mills
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA
| | - Taylor M Nichols
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA
| | - Charlotte H Abrahamson
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological Institute B486, Evanston, IL, 60208, USA.
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35
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Chen H, Wilson J, Ottinger S, Gan Q, Fan C. Introducing noncanonical amino acids for studying and engineering bacterial microcompartments. Curr Opin Microbiol 2021; 61:67-72. [PMID: 33813159 PMCID: PMC8169543 DOI: 10.1016/j.mib.2021.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/28/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
Bacterial microcompartments (BMCs) with selectively permeable shells and encapsulated enzyme cores are well-suited candidates for nano-bioreactors because of their advantages of enhancing pathway flux and protection against toxic products. To better study and engineer protein-based BMCs, a series of protein chemistry approaches are adopted. As one of the most advanced techniques, genetic code expansion can introduce various noncanonical amino acids (ncAAs) with diverse functional groups into target proteins, thus providing powerful tools for protein studies and engineering. This review summarizes and proposes useful tools based on current development of the genetic code expansion technique towards challenges in BMC studies and engineering.
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Affiliation(s)
- Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA
| | - Jessica Wilson
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA
| | - Sara Ottinger
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA; Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA.
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36
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Pokhrel A, Kang SY, Schmidt-Dannert C. Ethanolamine bacterial microcompartments: from structure, function studies to bioengineering applications. Curr Opin Microbiol 2021; 62:28-37. [PMID: 34034083 DOI: 10.1016/j.mib.2021.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022]
Abstract
Two decades of structural and functional studies have revealed functions, structures and diversity of bacterial microcompartments. The protein-based organelles encapsulate diverse metabolic pathways in semipermeable, icosahedral or pseudo-icosahedral shells. One of the first discovered and characterized microcompartments are those involved in ethanolamine degradation. This review will summarize their function and assembly along with shared and unique characteristics with other microcompartment types. The modularity and self-assembling properties of their shell proteins make them valuable targets for bioengineering. Advances and prospects for shell protein engineering in vivo and in vitro for synthetic biology and biotechnology applications will be discussed.
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Affiliation(s)
- Anaya Pokhrel
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Sun-Young Kang
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA.
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37
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Jenkins MC, Lutz S. Encapsulin Nanocontainers as Versatile Scaffolds for the Development of Artificial Metabolons. ACS Synth Biol 2021; 10:857-869. [PMID: 33769792 DOI: 10.1021/acssynbio.0c00636] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The construction of non-native biosynthetic pathways represents a powerful, modular strategy for the production of valuable synthons and fine chemicals. Accordingly, artificially affixing enzymes that catalyze sequential reactions onto DNAs, proteins, or synthetic scaffolds has proven to be an effective route for generating de novo metabolons with novel functionalities and superior efficiency. In recent years, nanoscale microbial compartments known as encapsulins have emerged as a class of robust and highly engineerable proteinaceous containers with myriad applications in biotechnology and synthetic biology. Herein we report the concurrent surface functionalization and internal packaging of encapsulins from Thermotoga maritima to generate a catalytically competent two-enzyme metabolon. Encapsulins were engineered to covalently sequester up to 60 copies of a dihydrofolate reductase (DHFR) enzyme variant on their exterior surfaces using the SpyCatcher bioconjugation system, while their lumens were packaged with a tetrahydrofolate-dependent demethylase enzyme using short peptide affinity tags abstracted from the encapsulin's native protein cargo. Successful cross-talk between the two colocalized enzymes was confirmed as tetrahydrofolate produced by externally tethered DHFR was capable of driving the demethylation of a lignin-derived aryl substrate by packaged demethylases, albeit slowly. The subsequent introduction of a previously reported pore-enlarging deletion in the encapsulin shell was shown to enhance metabolite exchange such that the encapsulin-based metabolon functioned at speeds equivalent to those of the two enzymes freely dispersed in solution. Our work thus further emphasizes the engineerability of encapsulins and their potential use as flexile scaffolds for biocatalytic applications.
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Affiliation(s)
- Matthew C. Jenkins
- Department of Chemistry, Emory University, Atlanta, Georgia 30084, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30306, United States
| | - Stefan Lutz
- Department of Chemistry, Emory University, Atlanta, Georgia 30084, United States
- Codexis Inc., 200 Penobscot Drive, Redwood City, California 94063, United States
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38
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Ochoa JM, Bair K, Holton T, Bobik TA, Yeates TO. MCPdb: The bacterial microcompartment database. PLoS One 2021; 16:e0248269. [PMID: 33780471 PMCID: PMC8007038 DOI: 10.1371/journal.pone.0248269] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
Bacterial microcompartments are organelle-like structures composed entirely of proteins. They have evolved to carry out several distinct and specialized metabolic functions in a wide variety of bacteria. Their outer shell is constructed from thousands of tessellating protein subunits, encapsulating enzymes that carry out the internal metabolic reactions. The shell proteins are varied, with single, tandem and permuted versions of the PF00936 protein family domain comprising the primary structural component of their polyhedral architecture, which is reminiscent of a viral capsid. While considerable amounts of structural and biophysical data have been generated in the last 15 years, the existing functionalities of current resources have limited our ability to rapidly understand the functional and structural properties of microcompartments (MCPs) and their diversity. In order to make the remarkable structural features of bacterial microcompartments accessible to a broad community of scientists and non-specialists, we developed MCPdb: The Bacterial Microcompartment Database (https://mcpdb.mbi.ucla.edu/). MCPdb is a comprehensive resource that categorizes and organizes known microcompartment protein structures and their larger assemblies. To emphasize the critical roles symmetric assembly and architecture play in microcompartment function, each structure in the MCPdb is validated and annotated with respect to: (1) its predicted natural assembly state (2) tertiary structure and topology and (3) the metabolic compartment type from which it derives. The current database includes 163 structures and is available to the public with the anticipation that it will serve as a growing resource for scientists interested in understanding protein-based metabolic organelles in bacteria.
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Affiliation(s)
- Jessica M. Ochoa
- UCLA Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Kaylie Bair
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Thomas Holton
- UCLA Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Thomas A. Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Todd O. Yeates
- UCLA Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
- UCLA Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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39
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Tan YQ, Xue B, Yew WS. Genetically Encodable Scaffolds for Optimizing Enzyme Function. Molecules 2021; 26:molecules26051389. [PMID: 33806660 PMCID: PMC7961827 DOI: 10.3390/molecules26051389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
Enzyme engineering is an indispensable tool in the field of synthetic biology, where enzymes are challenged to carry out novel or improved functions. Achieving these goals sometimes goes beyond modifying the primary sequence of the enzyme itself. The use of protein or nucleic acid scaffolds to enhance enzyme properties has been reported for applications such as microbial production of chemicals, biosensor development and bioremediation. Key advantages of using these assemblies include optimizing reaction conditions, improving metabolic flux and increasing enzyme stability. This review summarizes recent trends in utilizing genetically encodable scaffolds, developed in line with synthetic biology methodologies, to complement the purposeful deployment of enzymes. Current molecular tools for constructing these synthetic enzyme-scaffold systems are also highlighted.
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Affiliation(s)
- Yong Quan Tan
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Bo Xue
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Correspondence: ; Tel.: +65-6516-8624
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40
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Wilson JW. Manipulating microcompartment operons to study mechanism and function. Curr Opin Microbiol 2021; 60:66-72. [PMID: 33611144 DOI: 10.1016/j.mib.2021.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/21/2021] [Accepted: 01/27/2021] [Indexed: 12/26/2022]
Abstract
The gene systems that encode functional bacterial microcompartments (BMCs) are typically comprised of between 10-23 genes, often in a contiguous operon. BMC genes can be studied as whole native operons or as subsets of genes that form structures for specific applications. Recent examples of such studies highlight the flexible modular nature of BMC operons/genes and the options that exist to harness their functions via manipulation at the DNA level. This work also demonstrates the transfer and functional expression of BMC operons/genes across bacterial species. Recombineering, DNA synthesis technology, and advanced cloning techniques have all been applied in creative ways to study the nature of BMC mechanism and function.
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Affiliation(s)
- James W Wilson
- Department of Biology, Mendel Hall, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA.
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41
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Stewart AM, Stewart KL, Yeates TO, Bobik TA. Advances in the World of Bacterial Microcompartments. Trends Biochem Sci 2021; 46:406-416. [PMID: 33446424 DOI: 10.1016/j.tibs.2020.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/20/2022]
Abstract
Bacterial microcompartments (MCPs) are extremely large (100-400 nm) and diverse proteinaceous organelles that compartmentalize multistep metabolic pathways, increasing their efficiency and sequestering toxic and/or volatile intermediates. This review highlights recent studies that have expanded our understanding of the diversity, structure, function, and potential biotechnological uses of MCPs. Several new types of MCPs have been identified and characterized revealing new functions and potential new associations with human disease. Recent structural studies of MCP proteins and recombinant MCP shells have provided new insights into MCP assembly and mechanisms and raised new questions about MCP structure. We also discuss recent work on biotechnology applications that use MCP principles to develop nanobioreactors, nanocontainers, and molecular scaffolds.
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Affiliation(s)
- Andrew M Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Katie L Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA; UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA.
| | - Thomas A Bobik
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.
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42
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Liu LN. Bacterial metabolosomes: new insights into their structure and bioengineering. Microb Biotechnol 2021; 14:88-93. [PMID: 33404191 PMCID: PMC7888463 DOI: 10.1111/1751-7915.13740] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 12/18/2022] Open
Abstract
Bacterial metabolosomes have been discovered for over 25 years. They play essential roles in bacterial metabolism and pathogenesis. In this crystal ball paper, I will discuss the recent advances in the fundamental understanding and synthetic engineering of bacterial metabolosomes.
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Affiliation(s)
- Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.,College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
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43
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Kennedy NW, Ikonomova SP, Slininger Lee M, Raeder HW, Tullman-Ercek D. Self-assembling Shell Proteins PduA and PduJ have Essential and Redundant Roles in Bacterial Microcompartment Assembly. J Mol Biol 2020; 433:166721. [PMID: 33227310 DOI: 10.1016/j.jmb.2020.11.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 01/21/2023]
Abstract
Protein self-assembly is a common and essential biological phenomenon, and bacterial microcompartments present a promising model system to study this process. Bacterial microcompartments are large, protein-based organelles which natively carry out processes important for carbon fixation in cyanobacteria and the survival of enteric bacteria. These structures are increasingly popular with biological engineers due to their potential utility as nanobioreactors or drug delivery vehicles. However, the limited understanding of the assembly mechanism of these bacterial microcompartments hinders efforts to repurpose them for non-native functions. Here, we comprehensively investigate proteins involved in the assembly of the 1,2-propanediol utilization bacterial microcompartment from Salmonella enterica serovar Typhimurium LT2, one of the most widely studied microcompartment systems. We first demonstrate that two shell proteins, PduA and PduJ, have a high propensity for self-assembly upon overexpression, and we provide a novel method for self-assembly quantification. Using genomic knock-outs and knock-ins, we systematically show that these two proteins play an essential and redundant role in bacterial microcompartment assembly that cannot be compensated by other shell proteins. At least one of the two proteins PduA and PduJ must be present for the bacterial microcompartment shell to assemble. We also demonstrate that assembly-deficient variants of these proteins are unable to rescue microcompartment formation, highlighting the importance of this assembly property. Our work provides insight into the assembly mechanism of these bacterial organelles and will aid downstream engineering efforts.
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Affiliation(s)
- Nolan W Kennedy
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, United States
| | - Svetlana P Ikonomova
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - Marilyn Slininger Lee
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States; US Army Combat Capabilities Development Command Chemical Biological Center, Edgewood, MD, United States
| | - Henry W Raeder
- Molecular Biosciences Program, Weinberg College of Arts and Sciences, Northwestern University, Evanston, IL, United States
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States; Center for Synthetic Biology, Northwestern University, Evanston, IL, United States.
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44
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Groaz A, Moghimianavval H, Tavella F, Giessen TW, Vecchiarelli AG, Yang Q, Liu AP. Engineering spatiotemporal organization and dynamics in synthetic cells. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 13:e1685. [PMID: 33219745 DOI: 10.1002/wnan.1685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/13/2020] [Accepted: 10/30/2020] [Indexed: 12/28/2022]
Abstract
Constructing synthetic cells has recently become an appealing area of research. Decades of research in biochemistry and cell biology have amassed detailed part lists of components involved in various cellular processes. Nevertheless, recreating any cellular process in vitro in cell-sized compartments remains ambitious and challenging. Two broad features or principles are key to the development of synthetic cells-compartmentalization and self-organization/spatiotemporal dynamics. In this review article, we discuss the current state of the art and research trends in the engineering of synthetic cell membranes, development of internal compartmentalization, reconstitution of self-organizing dynamics, and integration of activities across scales of space and time. We also identify some research areas that could play a major role in advancing the impact and utility of engineered synthetic cells. This article is categorized under: Biology-Inspired Nanomaterials > Lipid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
| | | | | | | | | | - Qiong Yang
- University of Michigan, Ann Arbor, Michigan, USA
| | - Allen P Liu
- University of Michigan, Ann Arbor, Michigan, USA
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45
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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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46
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Stewart KL, Stewart AM, Bobik TA. Prokaryotic Organelles: Bacterial Microcompartments in E. coli and Salmonella. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0025-2019. [PMID: 33030141 PMCID: PMC7552817 DOI: 10.1128/ecosalplus.esp-0025-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Indexed: 02/07/2023]
Abstract
Bacterial microcompartments (MCPs) are proteinaceous organelles consisting of a metabolic pathway encapsulated within a selectively permeable protein shell. Hundreds of species of bacteria produce MCPs of at least nine different types, and MCP metabolism is associated with enteric pathogenesis, cancer, and heart disease. This review focuses chiefly on the four types of catabolic MCPs (metabolosomes) found in Escherichia coli and Salmonella: the propanediol utilization (pdu), ethanolamine utilization (eut), choline utilization (cut), and glycyl radical propanediol (grp) MCPs. Although the great majority of work done on catabolic MCPs has been carried out with Salmonella and E. coli, research outside the group is mentioned where necessary for a comprehensive understanding. Salient characteristics found across MCPs are discussed, including enzymatic reactions and shell composition, with particular attention paid to key differences between classes of MCPs. We also highlight relevant research on the dynamic processes of MCP assembly, protein targeting, and the mechanisms that underlie selective permeability. Lastly, we discuss emerging biotechnology applications based on MCP principles and point out challenges, unanswered questions, and future directions.
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Affiliation(s)
- Katie L. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Andrew M. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Thomas A. Bobik
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
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47
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Kerfeld CA, Sutter M. Engineered bacterial microcompartments: apps for programming metabolism. Curr Opin Biotechnol 2020; 65:225-232. [PMID: 32554213 PMCID: PMC7719235 DOI: 10.1016/j.copbio.2020.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022]
Abstract
Bacterial Microcompartments (BMCs) are used by diverse bacteria to compartmentalize enzymatic reactions, functioning analogously to the organelles of eukaryotes. The bounding membrane and encapsulated components are composed entirely of protein, which makes them ideal targets for modification by genetic engineering. In contrast to viruses, in which generally only one protein forms the capsid, the shells of BMCs consist of a variety of shell proteins, each a potential unit of selection. Despite their differences in permeability, the shell proteins are surprisingly interchangeable. Recent developments have shown that they are also highly amenable to engineered modifications which poise them for a variety of biotechnological applications. Given their modular structure, with a module defined as a semi-autonomous functional unit, BMCs can be considered apps for programming metabolism that can be de-bugged by adaptive evolution.
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Affiliation(s)
- Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory and Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory and Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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48
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Li C, Zhang R, Wang J, Wilson LM, Yan Y. Protein Engineering for Improving and Diversifying Natural Product Biosynthesis. Trends Biotechnol 2020; 38:729-744. [PMID: 31954530 PMCID: PMC7274900 DOI: 10.1016/j.tibtech.2019.12.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/26/2019] [Accepted: 12/06/2019] [Indexed: 01/26/2023]
Abstract
Proteins found in nature have traditionally been the most frequently used biocatalysts to produce numerous natural products ranging from commodity chemicals to pharmaceuticals. Protein engineering has emerged as a powerful biotechnological toolbox in the development of metabolic engineering, particularly for the biosynthesis of natural products. Recently, protein engineering has become a favored method to improve enzymatic activity, increase enzyme stability, and expand product spectra in natural product biosynthesis. This review summarizes recent advances and typical strategies in protein engineering, highlighting the paramount role of protein engineering in improving and diversifying the biosynthesis of natural products. Future prospects and research directions are also discussed.
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Affiliation(s)
- Chenyi Li
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Ruihua Zhang
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Jian Wang
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Lauren Marie Wilson
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yajun Yan
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA.
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49
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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50
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Demchuk AM, Patel TR. The biomedical and bioengineering potential of protein nanocompartments. Biotechnol Adv 2020; 41:107547. [PMID: 32294494 DOI: 10.1016/j.biotechadv.2020.107547] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 03/21/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022]
Abstract
Protein nanocompartments (PNCs) are self-assembling biological nanocages that can be harnessed as platforms for a wide range of nanobiotechnology applications. The most widely studied examples of PNCs include virus-like particles, bacterial microcompartments, encapsulin nanocompartments, enzyme-derived nanocages (such as lumazine synthase and the E2 component of the pyruvate dehydrogenase complex), ferritins and ferritin homologues, small heat shock proteins, and vault ribonucleoproteins. Structural PNC shell proteins are stable, biocompatible, and tolerant of both interior and exterior chemical or genetic functionalization for use as vaccines, therapeutic delivery vehicles, medical imaging aids, bioreactors, biological control agents, emulsion stabilizers, or scaffolds for biomimetic materials synthesis. This review provides an overview of the recent biomedical and bioengineering advances achieved with PNCs with a particular focus on recombinant PNC derivatives.
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Affiliation(s)
- Aubrey M Demchuk
- Department of Neuroscience, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, Canada.
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, Canada; Department of Microbiology, Immunology and Infectious Diseases, Cumming, School of Medicine, University of Calgary, 2500 University Dr. N.W., Calgary, AB T2N 1N4, Canada; Li Ka Shing Institute of Virology and Discovery Lab, Faculty of Medicine & Dentistry, University of Alberta, 6-010 Katz Center for Health Research, Edmonton, AB T6G 2E1, Canada.
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