1
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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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2
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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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3
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Kalnins G, Bertins M, Viksna A, Tars K. Functionalization of bacterial microcompartment shell interior with cysteine containing peptides enhances the iron and cobalt loading capacity. Biometals 2024; 37:267-274. [PMID: 37728832 DOI: 10.1007/s10534-023-00538-1] [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: 05/15/2023] [Accepted: 09/11/2023] [Indexed: 09/21/2023]
Abstract
Bacterial microcompartments (BMCs) are prokaryotic organelles involved in several biochemical processes in bacterial cells. These cellular substructures consist of an icosahedral shell and an encapsulated enzymatic core. The outer shells of BMCs have been proposed as an attractive platform for the creation of novel nanomaterials, nanocages, and nanoreactors. In this study, we present a method for functionalizing recombinant GRM2-type BMC shell lumens with short cysteine-containing sequences and demonstrate that the iron and cobalt loading capacity of such modified shells is markedly increased. These results also imply that a passive flow of cobalt and iron atoms across the BMC shell could be possible.
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Affiliation(s)
- Gints Kalnins
- Latvian Biomedical Research and Study Centre, Ratsupites street 1, Riga, 1067, Latvia.
| | - Maris Bertins
- University of Latvia, Jelgavas street 1, Riga, 1004, Latvia
| | - Arturs Viksna
- University of Latvia, Jelgavas street 1, Riga, 1004, Latvia
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites street 1, Riga, 1067, Latvia
- University of Latvia, Jelgavas street 1, Riga, 1004, Latvia
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4
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Ferlez BH, Kirst H, Greber BJ, Nogales E, Sutter M, Kerfeld CA. Heterologous Assembly of Pleomorphic Bacterial Microcompartment Shell Architectures Spanning the Nano- to Microscale. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2212065. [PMID: 36932732 PMCID: PMC10330516 DOI: 10.1002/adma.202212065] [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: 12/23/2022] [Revised: 03/09/2023] [Indexed: 06/09/2023]
Abstract
Many bacteria use protein-based organelles known as bacterial microcompartments (BMCs) to organize and sequester sequential enzymatic reactions. Regardless of their specialized metabolic function, all BMCs are delimited by a shell made of multiple structurally redundant, yet functionally diverse, hexameric (BMC-H), pseudohexameric/trimeric (BMC-T), or pentameric (BMC-P) shell protein paralogs. When expressed without their native cargo, shell proteins have been shown to self-assemble into 2D sheets, open-ended nanotubes, and closed shells of ≈40 nm diameter that are being developed as scaffolds and nanocontainers for applications in biotechnology. Here, by leveraging a strategy for affinity-based purification, it is demonstrated that a wide range of empty synthetic shells, many differing in end-cap structures, can be derived from a glycyl radical enzyme-associated microcompartment. The range of pleomorphic shells observed, which span ≈2 orders of magnitude in size from ≈25 nm to ≈1.8 µm, reveal the remarkable plasticity of BMC-based biomaterials. In addition, new capped nanotube and nanocone morphologies are observed that are consistent with a multicomponent geometric model in which architectural principles are shared among asymmetric carbon, viral protein, and BMC-based structures.
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Affiliation(s)
- Bryan H. Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Henning Kirst
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Basil J. Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Markus Sutter
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Cheryl A. Kerfeld
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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5
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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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6
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Mills CE, Waltmann C, Archer AG, Kennedy NW, Abrahamson CH, Jackson AD, Roth EW, Shirman S, Jewett MC, Mangan NM, Olvera de la Cruz M, Tullman-Ercek D. Vertex protein PduN tunes encapsulated pathway performance by dictating bacterial metabolosome morphology. Nat Commun 2022; 13:3746. [PMID: 35768404 PMCID: PMC9243111 DOI: 10.1038/s41467-022-31279-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 06/09/2022] [Indexed: 11/09/2022] Open
Abstract
Engineering subcellular organization in microbes shows great promise in addressing bottlenecks in metabolic engineering efforts; however, rules guiding selection of an organization strategy or platform are lacking. Here, we study compartment morphology as a factor in mediating encapsulated pathway performance. Using the 1,2-propanediol utilization microcompartment (Pdu MCP) system from Salmonella enterica serovar Typhimurium LT2, we find that we can shift the morphology of this protein nanoreactor from polyhedral to tubular by removing vertex protein PduN. Analysis of the metabolic function between these Pdu microtubes (MTs) shows that they provide a diffusional barrier capable of shielding the cytosol from a toxic pathway intermediate, similar to native MCPs. However, kinetic modeling suggests that the different surface area to volume ratios of MCP and MT structures alters encapsulated pathway performance. Finally, we report a microscopy-based assay that permits rapid assessment of Pdu MT formation to enable future engineering efforts on these structures. Morphology of metabolosomes affects the encapsulated pathway performance. Here, the authors combine experimental characterizations with structural and kinetic modeling to reveal how the shell protein PduN changes the morphology of 1,2-propanediol utilization (Pdu) metabolosome and how this morphology shift impacts Pdu function.
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Affiliation(s)
- Carolyn E Mills
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Curt Waltmann
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA
| | - Andre G Archer
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA
| | - Nolan W Kennedy
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Charlotte H Abrahamson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Alexander D Jackson
- Master of Science in Biotechnology Program, Northwestern University, Evanston, IL, USA
| | - Eric W Roth
- Northwestern University Atomic and Nanoscale Characterization Experimental Center, Evanston, IL, USA
| | - Sasha Shirman
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Niall M Mangan
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.,Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA. .,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
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7
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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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8
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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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9
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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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10
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Sasselli IR, Syrgiannis Z, Sather NA, Palmer LC, Stupp SI. Modeling Interactions within and between Peptide Amphiphile Supramolecular Filaments. J Phys Chem B 2022; 126:650-659. [PMID: 35029997 DOI: 10.1021/acs.jpcb.1c09258] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many peptides are able to self-assemble into one-dimensional (1D) nanostructures, such as cylindrical fibers or ribbons of variable widths, but the relationship between the morphology of 1D objects and their molecular structure is not well understood. Here, we use coarse-grained molecular dynamics (CG-MD) simulations to study the nanostructures formed by self-assembly of different peptide amphiphiles (PAs). The results show that ribbons are hierarchical superstructures formed by laterally assembled cylindrical fibers. Simulations starting from bilayer structures demonstrate the formation of filaments, whereas other simulations starting from filaments indicate varying degrees of interaction among them depending on chemical structure. These interactions are verified by observations using atomic force microscopy of the various systems. The interfilament interactions are predicted to be strongest in supramolecular assemblies that display hydrophilic groups on their surfaces, while those with hydrophobic ones are predicted to interact more weakly as confirmed by viscosity measurements. The simulations also suggest that peptide amphiphiles with hydrophobic termini bend to reduce their interfacial energy with water, which may explain why these systems do not collapse into superstructures of bundled filaments. The simulations suggest that future experiments will need to address mechanistic questions about the self-assembly of these systems into hierarchical structures, namely, the preformation of interactive filaments vs equilibration of large assemblies into superstructures.
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Affiliation(s)
- Ivan R Sasselli
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Zois Syrgiannis
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Nicholas A Sather
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Liam C Palmer
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Samuel I Stupp
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States.,Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States.,Department of Medicine, Northwestern University, 676 N St. Clair, Chicago, Illinois 60611, United States.,Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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11
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Gad S, Ayakar S. Protein scaffolds: A tool for multi-enzyme assembly. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 32:e00670. [PMID: 34824995 PMCID: PMC8605239 DOI: 10.1016/j.btre.2021.e00670] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/13/2021] [Accepted: 09/03/2021] [Indexed: 12/31/2022]
Abstract
The synthesis of complex molecules using multiple enzymes simultaneously in one reaction vessel has rapidly emerged as a new frontier in the field of bioprocess technology. However, operating different enzymes together in a single vessel limits their operational performance which needs to be addressed. With this respect, scaffolding proteins play an immense role in bringing different enzymes together in a specific manner. The scaffolding improves the catalytic performance, enzyme stability and provides an optimal micro-environment for biochemical reactions. This review describes the components of protein scaffolds, different ways of constructing a protein scaffold-based multi-enzyme complex, and their effects on enzyme kinetics. Moreover, different conjugation strategies viz; dockerin-cohesin interaction, SpyTag-SpyCatcher system, peptide linker-based ligation, affibody, and sortase-mediated ligation are discussed in detail. Various analytical and characterization tools that have enabled the development of these scaffolding strategies are also reviewed. Such mega-enzyme complexes promise wider applications in the field of biotechnology and bioengineering.
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Affiliation(s)
- Shubhada Gad
- Department of Biotechnology, Institute of Chemical Technology - IndianOil Odisha Campus Bhubaneswar, Odisha 751013, India
| | - Sonal Ayakar
- Department of Biotechnology, Institute of Chemical Technology - IndianOil Odisha Campus Bhubaneswar, Odisha 751013, India
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12
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Liu LN, Yang M, Sun Y, Yang J. Protein stoichiometry, structural plasticity and regulation of bacterial microcompartments. Curr Opin Microbiol 2021; 63:133-141. [PMID: 34340100 DOI: 10.1016/j.mib.2021.07.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/17/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022]
Abstract
Bacterial microcompartments (BMCs) are self-assembling prokaryotic organelles consisting of a polyhedral proteinaceous shell and encapsulated enzymes that are involved in CO2 fixation or carbon catabolism. Addressing how the hundreds of building components self-assemble to form the metabolically functional organelles and how their structures and functions are modulated in the extremely dynamic bacterial cytoplasm is of importance for basic understanding of protein organelle formation and synthetic engineering of metabolic modules for biotechnological applications. Here, we highlight recent advances in understanding the protein composition and stoichiometry of BMCs, with a particular focus on carboxysomes and propanediol utilization microcompartments. We also discuss relevant research on the structural plasticity of native and engineered BMCs, and the physiological regulation of BMC assembly, function and positioning in native hosts.
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Affiliation(s)
- Lu-Ning Liu
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 266003 Qingdao, China; Institute of Systems Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.
| | - Mengru Yang
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Yaqi Sun
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Jing Yang
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom; Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, United Kingdom
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13
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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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14
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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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15
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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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16
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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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17
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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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18
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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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19
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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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20
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Nichols TM, Kennedy NW, Tullman-Ercek D. A genomic integration platform for heterologous cargo encapsulation in 1,2-propanediol utilization bacterial microcompartments. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107496] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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Apparent size and morphology of bacterial microcompartments varies with technique. PLoS One 2020; 15:e0226395. [PMID: 32150579 PMCID: PMC7062276 DOI: 10.1371/journal.pone.0226395] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 02/25/2020] [Indexed: 12/30/2022] Open
Abstract
Bacterial microcompartments (MCPs) are protein-based organelles that encapsulate metabolic pathways. Metabolic engineers have recently sought to repurpose MCPs to encapsulate heterologous pathways to increase flux through pathways of interest. As MCP engineering becomes more common, standardized methods for analyzing changes to MCPs and interpreting results across studies will become increasingly important. In this study, we demonstrate that different imaging techniques yield variations in the apparent size of purified MCPs from Salmonella enterica serovar Typhimurium LT2, likely due to variations in sample preparation methods. We provide guidelines for preparing samples for MCP imaging and outline expected variations in apparent size and morphology between methods. With this report we aim to establish an aid for comparing results across studies.
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22
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Edgell CL, Smith AJ, Beesley JL, Savery NJ, Woolfson DN. De Novo Designed Protein-Interaction Modules for In-Cell Applications. ACS Synth Biol 2020; 9:427-436. [PMID: 31977192 DOI: 10.1021/acssynbio.9b00453] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein-protein interactions control a wide variety of natural biological processes. α-Helical coiled coils frequently mediate such protein-protein interactions. Due to the relative simplicity of their sequences and structures and the ease with which properties such as strength and specificity of interaction can be controlled, coiled coils can be designed de novo to deliver a variety of non-natural protein-protein interaction domains. Herein, several de novo designed coiled coils are tested for their ability to mediate protein-protein interactions in Escherichia coli cells. The set includes a parallel homodimer, a parallel homotetramer, an antiparallel homotetramer, and a newly designed heterotetramer, all of which have been characterized in vitro by biophysical and structural methods. Using a transcription repression assay based on reconstituting the Lac repressor, we find that the modules behave as designed in the cellular environment. Each design imparts a different property to the resulting Lac repressor-coiled coil complexes, resulting in the benefit of being able to reconfigure the system in multiple ways. Modification of the system also allows the interactions to be controlled: assembly can be tuned by controlling the expression of the constituent components, and complexes can be disrupted through helix sequestration. The small and straightforward de novo designed components that we deliver are highly versatile and have considerable potential as protein-protein interaction domains in synthetic biology where proteins must be assembled in highly specific ways. The relative simplicity of the designs makes them amenable to future modifications to introduce finer control over their assembly and to adapt them for different contexts.
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Affiliation(s)
- Caitlin L. Edgell
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Abigail J. Smith
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
- BrisSynBio, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, United Kingdom
| | - Joseph L. Beesley
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Nigel J. Savery
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
- BrisSynBio, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, United Kingdom
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
- BrisSynBio, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, United Kingdom
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23
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Kalnins G, Cesle EE, Jansons J, Liepins J, Filimonenko A, Tars K. Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles. Nat Commun 2020; 11:388. [PMID: 31959751 PMCID: PMC6971018 DOI: 10.1038/s41467-019-14205-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/18/2019] [Indexed: 11/08/2022] Open
Abstract
Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We conclude that the enzymatic core is encapsulated in a hierarchical manner and that the CutC choline lyase may play a secondary role as an adaptor protein. We also present a cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle at 3.3 Å resolution, and demonstrate variability among the minor shell forms.
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Affiliation(s)
- Gints Kalnins
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia.
| | - Eva-Emilija Cesle
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
| | - Juris Jansons
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, Riga, 1004, Latvia
| | - Anatolij Filimonenko
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
- University of Latvia, Jelgavas 1, Riga, 1004, Latvia
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24
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Young EJ, Sakkos JK, Huang J, Wright JK, Kachel B, Fuentes-Cabrera M, Kerfeld CA, Ducat DC. Visualizing in Vivo Dynamics of Designer Nanoscaffolds. NANO LETTERS 2020; 20:208-217. [PMID: 31747755 DOI: 10.1021/acs.nanolett.9b03651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Enzymes of natural biochemical pathways are routinely subcellularly organized in space and time in order to improve pathway efficacy and control. Designer scaffolding platforms are under development to confer similar benefits upon engineered pathways. Herein, we evaluate bacterial microcompartment shell (pfam0936-domain) proteins as modules for constructing well-defined nanometer scale scaffolds in vivo. We use a suite of visualization techniques to evaluate scaffold assembly and dynamics. We demonstrate recruitment of target cargo molecules onto assembled scaffolds by appending reciprocally interacting adaptor domains. These interactions can be refined by fine-tuning the scaffold expression level. Real-time observation of this system reveals a nucleation-limited step where multiple scaffolds initially form within a cell. Over time, nucleated scaffolds reorganize into a single intracellular assembly, likely due to interscaffold competition for protein subunits. Our results suggest design considerations for using self-assembling proteins as building blocks to construct nanoscaffolds, while also providing a platform to visualize scaffold-cargo dynamics in vivo.
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Affiliation(s)
- Eric J Young
- MSU-DOE Plant Research Laboratory , Michigan State University , East Lansing , Michigan 48824 United States
- Department of Biochemistry & Molecular Biology , Michigan State University , East Lansing , Michigan 48824 United States
| | - Jonathan K Sakkos
- MSU-DOE Plant Research Laboratory , Michigan State University , East Lansing , Michigan 48824 United States
- Department of Biochemistry & Molecular Biology , Michigan State University , East Lansing , Michigan 48824 United States
| | - Jingcheng Huang
- MSU-DOE Plant Research Laboratory , Michigan State University , East Lansing , Michigan 48824 United States
- Department of Biochemistry & Molecular Biology , Michigan State University , East Lansing , Michigan 48824 United States
| | - Jacob K Wright
- MSU-DOE Plant Research Laboratory , Michigan State University , East Lansing , Michigan 48824 United States
- Department of Biochemistry & Molecular Biology , Michigan State University , East Lansing , Michigan 48824 United States
| | - Benjamin Kachel
- Institute for Technical Microbiology , Mannheim University of Applied Sciences , Mannheim , Germany
| | - Miguel Fuentes-Cabrera
- Computational Sciences and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37830 United States
- Center for Nanophase Material Sciences Oak Ridge National Laboratory , Oak Ridge , Tennessee 37830 United States
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory , Michigan State University , East Lansing , Michigan 48824 United States
- Department of Biochemistry & Molecular Biology , Michigan State University , East Lansing , Michigan 48824 United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions , Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
| | - Daniel C Ducat
- MSU-DOE Plant Research Laboratory , Michigan State University , East Lansing , Michigan 48824 United States
- Department of Biochemistry & Molecular Biology , Michigan State University , East Lansing , Michigan 48824 United States
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25
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Plegaria JS, Yates MD, Glaven SM, Kerfeld CA. Redox Characterization of Electrode-Immobilized Bacterial Microcompartment Shell Proteins Engineered To Bind Metal Centers. ACS APPLIED BIO MATERIALS 2019; 3:685-692. [DOI: 10.1021/acsabm.9b01023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | - Matthew D. Yates
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Sarah M. Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Cheryl A. Kerfeld
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
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26
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Kirst H, Kerfeld CA. Bacterial microcompartments: catalysis-enhancing metabolic modules for next generation metabolic and biomedical engineering. BMC Biol 2019; 17:79. [PMID: 31601225 PMCID: PMC6787980 DOI: 10.1186/s12915-019-0691-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022] Open
Abstract
Bacterial cells have long been thought to be simple cells with little spatial organization, but recent research has shown that they exhibit a remarkable degree of subcellular differentiation. Indeed, bacteria even have organelles such as magnetosomes for sensing magnetic fields or gas vesicles controlling cell buoyancy. A functionally diverse group of bacterial organelles are the bacterial microcompartments (BMCs) that fulfill specialized metabolic needs. Modification and reengineering of these BMCs enable innovative approaches for metabolic engineering and nanomedicine.
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Affiliation(s)
- Henning Kirst
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA.,Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA. .,Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA. .,Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI, 48824, USA.
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27
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Wade Y, Daniel RA, Leak DJ. Heterologous Microcompartment Assembly in Bacillaceae: Establishing the Components Necessary for Scaffold Formation. ACS Synth Biol 2019; 8:1642-1654. [PMID: 31242391 DOI: 10.1021/acssynbio.9b00155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacterial microcompartments (BMCs) are organelles that host specific biochemical reactions for both anabolic and catabolic functions. Engineered morphologically diverse BMCs bearing heterologous enzymatic pathways have shown enhanced productivity for commodity chemicals, which makes BMCs an important focus for metabolic engineering. Gaining control of BMC assembly and incorporation of a heterologous enzymatic cargo has yet to be achieved in thermophiles. Herein, we address this by first conducting a detailed bioinformatic analysis of the propanediol utilization (pdu) operon in the thermophile Parageobacillus thermoglucosidasius. We then demonstrated, in vivo, the ability to assemble the native BMCs at an elevated temperature of 60 °C. Heterologous expression of Pdu shell proteins from P. thermoglucosidasius in Bacillus subtilis resulted in the assembly of a single tubular BMC with an average length of 1.4 μm; BMCs assembled after a 20 min induction of expression of the shell operons. Moreover, we show that it is possible to target the monomeric superfolder GFP (msfGFP) to the interior of the compartment by fusion of an N-terminal sequence of the propanediol utilization protein (PduP) of at least 24 amino acids. This study establishes the feasibility of constructing cell factories for small molecules in industrially important Bacillus and Geobacillus spp. by heterologous cargo-carrying BMC production and assembly. Additionally, the study provides experimental confirmation that BMCs are produced in thermophilic bacteria, which opens a path for future research on repurposing the native organelles to provide new functionality at elevated temperatures.
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Affiliation(s)
- Yana Wade
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle-upon-Tyne, NE2 4AX, U.K
| | - Richard A. Daniel
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle-upon-Tyne, NE2 4AX, U.K
| | - David J. Leak
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K
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Bio-engineering of bacterial microcompartments: a mini review. Biochem Soc Trans 2019; 47:765-777. [DOI: 10.1042/bst20170564] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/09/2019] [Accepted: 05/22/2019] [Indexed: 12/30/2022]
Abstract
AbstractBacterial microcompartments (BMCs) are protein-bound prokaryotic organelles, discovered in cyanobacteria more than 60 years ago. Functionally similar to eukaryotic cellular organelles, BMCs compartment metabolic activities in the cytoplasm, foremost to increase local enzyme concentration and prevent toxic intermediates from damaging the cytosolic content. Advanced knowledge of the functional and structural properties of multiple types of BMCs, particularly over the last 10 years, have highlighted design principles of microcompartments. This has prompted new research into their potential to function as programmable synthetic nano-bioreactors and novel bio-materials with biotechnological and medical applications. Moreover, due to the involvement of microcompartments in bacterial pathogenesis and human health, BMCs have begun to gain attention as potential novel drug targets. This mini-review gives an overview of important synthetic biology developments in the bioengineering of BMCs and a perspective on future directions in the field.
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Smith AJ, Thomas F, Shoemark D, Woolfson DN, Savery NJ. Guiding Biomolecular Interactions in Cells Using de Novo Protein-Protein Interfaces. ACS Synth Biol 2019; 8:1284-1293. [PMID: 31059644 DOI: 10.1021/acssynbio.8b00501] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
An improved ability to direct and control biomolecular interactions in living cells would have an impact on synthetic biology. A key issue is the need to introduce interacting components that act orthogonally to endogenous proteomes and interactomes. Here, we show that low-complexity, de novo designed protein-protein interaction (PPI) domains can substitute for natural PPIs and guide engineered protein-DNA interactions in Escherichia coli. Specifically, we use de novo homo- and heterodimeric coiled coils to reconstitute a cytoplasmic split adenylate cyclase, recruit RNA polymerase to a promoter and activate gene expression, and oligomerize both natural and designed DNA-binding domains to repress transcription. Moreover, the stabilities of the heterodimeric coiled coils can be modulated by rational design and, thus, adjust the levels of gene activation and repression in vivo. These experiments demonstrate the possibilities for using designed proteins and interactions to control biomolecular systems such as enzyme cascades and circuits in cells.
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Affiliation(s)
- Abigail J. Smith
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Franziska Thomas
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Deborah Shoemark
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Derek N. Woolfson
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Nigel J. Savery
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
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30
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A designed bacterial microcompartment shell with tunable composition and precision cargo loading. Metab Eng 2019; 54:286-291. [PMID: 31075444 DOI: 10.1016/j.ymben.2019.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/09/2019] [Accepted: 04/24/2019] [Indexed: 12/31/2022]
Abstract
Microbes often augment their metabolism by conditionally constructing proteinaceous organelles, known as bacterial microcompartments (BMCs), that encapsulate enzymes to degrade organic compounds or assimilate CO2. BMCs self-assemble and are spatially delimited by a semi-permeable shell made up of hexameric, trimeric, and pentameric shell proteins. Bioengineers aim to recapitulate the organization and efficiency of these complex biological architectures by redesigning the shell to incorporate non-native enzymes from biotechnologically relevant pathways. To meet this challenge, a diverse set of synthetic biology tools are required, including methods to manipulate the properties of the shell as well as target and organize cargo encapsulation. We designed and determined the crystal structure of a synthetic shell protein building block with an inverted sidedness of its N- and C-terminal residues relative to its natural counterpart; the inversion targets genetically fused protein cargo to the lumen of the shell. Moreover, the titer of fluorescent protein cargo encapsulated using this strategy is controllable using an inducible tetracycline promoter. These results expand the available set of building blocks for precision engineering of BMC-based nanoreactors and are compatible with orthogonal methods which will facilitate the installation and organization of multi-enzyme pathways.
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31
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Beesley JL, Woolfson DN. The de novo design of α-helical peptides for supramolecular self-assembly. Curr Opin Biotechnol 2019; 58:175-182. [PMID: 31039508 DOI: 10.1016/j.copbio.2019.03.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 03/25/2019] [Indexed: 12/14/2022]
Abstract
One approach to designing de novo proteinaceous assemblies and materials is to develop simple, standardised building blocks and then to combine these symmetrically to construct more-complex higher-order structures. This has been done extensively using β-structured peptides to produce peptide fibres and hydrogels. Here, we focus on building with de novo α-helical peptides. Because of their self-contained, well-defined structures and clear sequence-to-structure relationships, α helices are highly programmable making them robust building blocks for biomolecular construction. The progress made with this approach over the past two decades is astonishing and has led to a variety of de novo assemblies, including discrete nanoscale objects, and fibrous, nanotube, sheet and colloidal materials. This body of work provides an exceptionally strong foundation for advancing the field beyond in vitro design and into in vivo applications including what we call protein design in cells.
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Affiliation(s)
- Joseph L Beesley
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK; BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
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Smirnoff N. Engineering of Metabolic Pathways Using Synthetic Enzyme Complexes. PLANT PHYSIOLOGY 2019; 179:918-928. [PMID: 30455287 PMCID: PMC6393806 DOI: 10.1104/pp.18.01280] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 11/01/2018] [Indexed: 05/20/2023]
Abstract
Prospects are reviewed for the use of synthetic enzyme complexes as a metabolic engineering tool.
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Affiliation(s)
- Nicholas Smirnoff
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, United Kingdom
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Biotechnological Advances in Bacterial Microcompartment Technology. Trends Biotechnol 2018; 37:325-336. [PMID: 30236905 DOI: 10.1016/j.tibtech.2018.08.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 12/22/2022]
Abstract
Bacterial microcompartments (BMCs) represent proteinaceous macromolecular nanobioreactors that are found in a broad range of bacteria, and which are associated with either anabolic or catabolic processes. They consist of a semipermeable outer shell that packages a central metabolic enzyme or pathway, providing both enhanced flux and protection against toxic intermediates. Recombinant production of BMCs has led to their repurposing with the incorporation of altogether new pathways. Deconstructing BMCs into their component parts has shown that some individual shell proteins self-associate into filaments that can be further modified into a cytoplasmic scaffold, or cytoscaffold, to which enzymes/proteins can be targeted. BMCs therefore represent a modular system that is highly suited for engineering biological systems for useful purposes.
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