1
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Zhou RQ, Jiang YL, Li H, Hou P, Kong WW, Deng JX, Chen Y, Zhou CZ, Zeng Q. Structure and assembly of the α-carboxysome in the marine cyanobacterium Prochlorococcus. Nat Plants 2024; 10:661-672. [PMID: 38589484 DOI: 10.1038/s41477-024-01660-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/29/2024] [Indexed: 04/10/2024]
Abstract
Carboxysomes are bacterial microcompartments that encapsulate the enzymes RuBisCO and carbonic anhydrase in a proteinaceous shell to enhance the efficiency of photosynthetic carbon fixation. The self-assembly principles of the intact carboxysome remain elusive. Here we purified α-carboxysomes from Prochlorococcus and examined their intact structures using single-particle cryo-electron microscopy to solve the basic principles of their shell construction and internal RuBisCO organization. The 4.2 Å icosahedral-like shell structure reveals 24 CsoS1 hexamers on each facet and one CsoS4A pentamer at each vertex. RuBisCOs are organized into three concentric layers within the shell, consisting of 72, 32 and up to 4 RuBisCOs at the outer, middle and inner layers, respectively. We uniquely show how full-length and shorter forms of the scaffolding protein CsoS2 bind to the inner surface of the shell via repetitive motifs in the middle and C-terminal regions. Combined with previous reports, we propose a concomitant 'outside-in' assembly principle of α-carboxysomes: the inner surface of the self-assembled shell is reinforced by the middle and C-terminal motifs of the scaffolding protein, while the free N-terminal motifs cluster to recruit RuBisCO in concentric, three-layered spherical arrangements. These new insights into the coordinated assembly of α-carboxysomes may guide the rational design and repurposing of carboxysome structures for improving plant photosynthetic efficiency.
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Affiliation(s)
- Rui-Qian Zhou
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yong-Liang Jiang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Haofu Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Pu Hou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wen-Wen Kong
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Jia-Xin Deng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yuxing Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Cong-Zhao Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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2
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Raza S, Sarkar D, Chan LJG, Mae J, Sutter M, Petzold CJ, Kerfeld CA, Ralston CY, Gupta S, Vermaas JV. Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells. bioRxiv 2024:2024.03.12.584231. [PMID: 38559214 PMCID: PMC10980050 DOI: 10.1101/2024.03.12.584231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semi-permeable shell proteins, analogous to many membrane-bound organelles. The shell proteins assemble into multimeric tiles; hexamers, trimers, and pentamers, and these tiles self-assemble into larger assemblies with icosahedral symmetry. While icosahedral shells are the predominant form in vivo, the tiles can also form nanoscale cylinders or sheets. The individual multimeric tiles feature central pores that are key to regulating transport across the protein shell. Our primary interest is to quantify pore shape changes in response to alternative component morphologies at the nanoscale. We use molecular modeling tools to develop atomically detailed models for both planar sheets of tiles and curved structures representative of the complete shells found in vivo. Subsequently, these models were animated using classical molecular dynamics simulations. From the resulting trajectories, we analyzed overall structural stability, water accessibility to individual residues, water residence time, and pore geometry for the hexameric and trimeric protein tiles from the Haliangium ochraceum model BMC shell. These exhaustive analyses suggest no substantial variation in pore structure or solvent accessibility between the flat and curved shell geometries. We additionally compare our analysis to hydroxyl radical footprinting data to serve as a check against our simulation results, highlighting specific residues where water molecules are bound for a long time. Although with little variation in morphology or water interaction, we propose that the planar and capsular morphology can be used interchangeably when studying permeability through BMC pores.
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Affiliation(s)
- Saad Raza
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
| | - Daipayan Sarkar
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
| | - Leanne Jade G Chan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Current address: Calico Life Sciences LLC, South San Francisco, CA 94080
| | - Joshua Mae
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
- Department Of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720
| | - Corie Y Ralston
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720
| | - Josh V Vermaas
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
- Department Of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824
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3
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Trettel DS, Pacheco SL, Laskie AK, Gonzalez-Esquer CR. Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Ni T, Jiang Q, Ng PC, Shen J, Dou H, Zhu Y, Radecke J, Dykes GF, Huang F, Liu LN, Zhang P. Intrinsically disordered CsoS2 acts as a general molecular thread for α-carboxysome shell assembly. Nat Commun 2023; 14:5512. [PMID: 37679318 PMCID: PMC10484944 DOI: 10.1038/s41467-023-41211-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 08/27/2023] [Indexed: 09/09/2023] Open
Abstract
Carboxysomes are a paradigm of self-assembling proteinaceous organelles found in nature, offering compartmentalisation of enzymes and pathways to enhance carbon fixation. In α-carboxysomes, the disordered linker protein CsoS2 plays an essential role in carboxysome assembly and Rubisco encapsulation. Its mechanism of action, however, is not fully understood. Here we synthetically engineer α-carboxysome shells using minimal shell components and determine cryoEM structures of these to decipher the principle of shell assembly and encapsulation. The structures reveal that the intrinsically disordered CsoS2 C-terminus is well-structured and acts as a universal "molecular thread" stitching through multiple shell protein interfaces. We further uncover in CsoS2 a highly conserved repetitive key interaction motif, [IV]TG, which is critical to the shell assembly and architecture. Our study provides a general mechanism for the CsoS2-governed carboxysome shell assembly and cargo encapsulation and further advances synthetic engineering of carboxysomes for diverse biotechnological applications.
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Affiliation(s)
- Tao Ni
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Pei Cing Ng
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Juan Shen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Hao Dou
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Yanan Zhu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Julika Radecke
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Fang Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China.
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK.
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6
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Waltmann C, Kennedy NW, Mills CE, Roth EW, Ikonomova SP, Tullman-Ercek D, Olvera de la Cruz M. Kinetic Growth of Multicomponent Microcompartment Shells. ACS Nano 2023; 17:15751-15762. [PMID: 37552700 DOI: 10.1021/acsnano.3c03353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Overall, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.
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Affiliation(s)
- Curt Waltmann
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Nolan W Kennedy
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Carolyn E Mills
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Eric W Roth
- Northwestern University Atomic and Nanoscale Characterization Experimentation Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Svetlana P Ikonomova
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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7
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Evans SL, Al-Hazeem MMJ, Mann D, Smetacek N, Beavil AJ, Sun Y, Chen T, Dykes GF, Liu LN, Bergeron JRC. Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact α-carboxysome. Structure 2023; 31:677-688.e4. [PMID: 37015227 PMCID: PMC10689251 DOI: 10.1016/j.str.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/19/2023] [Accepted: 03/09/2023] [Indexed: 04/05/2023]
Abstract
Carboxysomes are proteinaceous bacterial microcompartments that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, encapsulating several enzymes, including ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for the first step of the Calvin-Benson-Bassham cycle. Despite their significance in carbon fixation and great bioengineering potentials, the structural understanding of native carboxysomes is currently limited to low-resolution studies. Here, we report the characterization of a native α-carboxysome from a marine cyanobacterium by single-particle cryoelectron microscopy (cryo-EM). We have determined the structure of its RuBisCO enzyme, and obtained low-resolution maps of its icosahedral shell, and of its concentric interior organization. Using integrative modeling approaches, we have proposed a complete atomic model of an intact carboxysome, providing insight into its organization and assembly. This is critical for a better understanding of the carbon fixation mechanism and toward repurposing carboxysomes in synthetic biology for biotechnological applications.
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Affiliation(s)
- Sasha L Evans
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Monsour M J Al-Hazeem
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daniel Mann
- Ernst-Ruska Centre 3, Forschungszentrum Jülich, Jülich, Germany
| | - Nicolas Smetacek
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - Andrew J Beavil
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, Shandong, China.
| | - Julien R C Bergeron
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK; Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK.
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8
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Huffine CA, Zhao R, Tang YJ, Cameron JC. Role of carboxysomes in cyanobacterial CO 2 assimilation: CO 2 concentrating mechanisms and metabolon implications. Environ Microbiol 2023; 25:219-228. [PMID: 36367380 DOI: 10.1111/1462-2920.16283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
Many carbon-fixing organisms have evolved CO2 concentrating mechanisms (CCMs) to enhance the delivery of CO2 to RuBisCO, while minimizing reactions with the competitive inhibitor, molecular O2 . These distinct types of CCMs have been extensively studied using genetics, biochemistry, cell imaging, mass spectrometry, and metabolic flux analysis. Highlighted in this paper, the cyanobacterial CCM features a bacterial microcompartment (BMC) called 'carboxysome' in which RuBisCO is co-encapsulated with the enzyme carbonic anhydrase (CA) within a semi-permeable protein shell. The cyanobacterial CCM is capable of increasing CO2 around RuBisCO, leading to one of the most efficient processes known for fixing ambient CO2 . The carboxysome life cycle is dynamic and creates a unique subcellular environment that promotes activity of the Calvin-Benson (CB) cycle. The carboxysome may function within a larger cellular metabolon, physical association of functionally coupled proteins, to enhance metabolite channelling and carbon flux. In light of CCMs, synthetic biology approaches have been used to improve enzyme complex for CO2 fixations. Research on CCM-associated metabolons has also inspired biologists to engineer multi-step pathways by providing anchoring points for enzyme cascades to channel intermediate metabolites towards valuable products.
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Affiliation(s)
- Clair A Huffine
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, Colorado, USA
- Interdisciplinary Quantitative Biology Program (IQ Biology), BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA
| | - Runyu Zhao
- Department of Energy, Environmental and Chemical Engineering, Washington University in Saint Louis, Saint Louis, Missouri, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University in Saint Louis, Saint Louis, Missouri, USA
| | - Jeffrey C Cameron
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, Colorado, USA
- National Renewable Energy Laboratory, Golden, Colorado, USA
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9
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Metskas LA, Ortega D, Oltrogge LM, Blikstad C, Lovejoy DR, Laughlin TG, Savage DF, Jensen GJ. Rubisco forms a lattice inside alpha-carboxysomes. Nat Commun 2022; 13:4863. [PMID: 35982043 DOI: 10.1038/s41467-022-32584-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 08/04/2022] [Indexed: 02/07/2023] Open
Abstract
Despite the importance of microcompartments in prokaryotic biology and bioengineering, structural heterogeneity has prevented a complete understanding of their architecture, ultrastructure, and spatial organization. Here, we employ cryo-electron tomography to image α-carboxysomes, a pseudo-icosahedral microcompartment responsible for carbon fixation. We have solved a high-resolution subtomogram average of the Rubisco cargo inside the carboxysome, and determined the arrangement of the enzyme. We find that the H. neapolitanus Rubisco polymerizes in vivo, mediated by the small Rubisco subunit. These fibrils can further pack to form a lattice with six-fold pseudo-symmetry. This arrangement preserves freedom of motion and accessibility around the Rubisco active site and the binding sites for two other carboxysome proteins, CsoSCA (a carbonic anhydrase) and the disordered CsoS2, even at Rubisco concentrations exceeding 800 μM. This characterization of Rubisco cargo inside the α-carboxysome provides insight into the balance between order and disorder in microcompartment organization.
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Abstract
Self-assembling proteins can form porous compartments that adopt well-defined architectures at the nanoscale. In nature, protein compartments act as semipermeable barriers to enable spatial separation and organization of complex biochemical processes. The compartment pores play a key role in their overall function by selectively controlling the influx and efflux of important biomolecular species. By engineering the pores, the functionality of compartments can be tuned to facilitate non-native applications, such as artificial nanoreactors for catalysis. In this review, we analyze how protein structure determines the porosity and impacts the function of both native and engineered compartments, highlighting the wealth of structural data recently obtained by cryo-EM and X-ray crystallography. Through this analysis, we offer perspectives on how current structural insights can inform future studies into the design of artificial protein compartments as nanoreactors with tunable porosity and function.
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Affiliation(s)
- Nuren Tasneem
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
| | - Taylor N Szyszka
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
- University of Sydney Nano Institute, Camperdown, New South Wales 2006, Australia
| | - Eric N Jenner
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
- University of Sydney Nano Institute, Camperdown, New South Wales 2006, Australia
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12
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Kennedy NW, Mills CE, Abrahamson CH, Archer AG, Shirman S, Jewett MC, Mangan NM, Tullman-Ercek D. Linking the Salmonella enterica 1,2-Propanediol Utilization Bacterial Microcompartment Shell to the Enzymatic Core via the Shell Protein PduB. J Bacteriol 2022;:e0057621. [PMID: 35575582 DOI: 10.1128/jb.00576-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [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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13
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Chen T, Fang Y, Jiang Q, Dykes GF, Lin Y, Price GD, Long BM, Liu LN. Incorporation of Functional Rubisco Activases into Engineered Carboxysomes to Enhance Carbon Fixation. ACS Synth Biol 2022; 11:154-161. [PMID: 34664944 PMCID: PMC8787814 DOI: 10.1021/acssynbio.1c00311] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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The carboxysome is
a versatile paradigm of prokaryotic organelles
and is a proteinaceous self-assembling microcompartment that plays
essential roles in carbon fixation in all cyanobacteria and some chemoautotrophs.
The carboxysome encapsulates
the central CO2-fixing enzyme, ribulose-1,5-bisphosphate
carboxylase/oxygenase (Rubisco), using a polyhedral protein shell
that is selectively permeable to specific metabolites in favor of
Rubisco carboxylation. There is tremendous interest in repurposing
carboxysomes to boost carbon fixation in heterologous organisms. Here,
we develop the design and engineering of α-carboxysomes by coexpressing
the Rubisco activase components CbbQ and CbbO with α-carboxysomes
in Escherichia coli. Our results show
that CbbQ and CbbO could assemble into the reconstituted α-carboxysome
as intrinsic components. Incorporation of both CbbQ and CbbO within
the carboxysome promotes activation of Rubisco and enhances the CO2-fixation activities of recombinant carboxysomes. We also
show that the structural composition of these carboxysomes could be
modified in different expression systems, representing the plasticity
of the carboxysome architecture. In translational terms, our study
informs strategies for engineering and modulating carboxysomes in
diverse biotechnological applications.
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Affiliation(s)
- Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Fang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Gregory F. Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - G. Dean Price
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory 2601, Australia
| | - Benedict M. Long
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory 2601, Australia
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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14
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Abstract
Carboxysomes are a family of bacterial microcompartments (BMCs), present in all cyanobacteria and some proteobacteria, which encapsulate the primary CO2-fixing enzyme, Rubisco, within a virus-like polyhedral protein shell. Carboxysomes provide significantly elevated levels of CO2 around Rubisco to maximize carboxylation and reduce wasteful photorespiration, thus functioning as the central CO2-fixation organelles of bacterial CO2-concentration mechanisms. Their intriguing architectural features allow carboxysomes to make a vast contribution to carbon assimilation on a global scale. In this review, we discuss recent research progress that provides new insights into the mechanisms of how carboxysomes are assembled and functionally maintained in bacteria and recent advances in synthetic biology to repurpose the metabolic module in diverse applications.
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Affiliation(s)
- Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 266003 Qingdao, China.
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15
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Abstract
We introduce Viral Phrenology, a new scheme for understanding the genomic composition of spherical viruses based on the locations of their structural protrusions. We used icosahedral point arrays to classify 135 distinct viral capsids collected from over 600 capsids available in the VIPERdb. Using gauge points of point arrays, we found 149 unique structural protrusions. We then show how to use the locations of these protrusions to determine the genetic composition of the virus. We then show that ssDNA, dsDNA, dsRNA and ssRNA viruses use different arrangements for distributing their protrusions. We also found that Triangulation number is also partially dependent on the structural protrusions. This analysis begins to tie together Baltimore Classification and Triangulation number using point arrays.
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16
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Melnicki MR, Sutter M, Kerfeld CA. Evolutionary relationships among shell proteins of carboxysomes and metabolosomes. Curr Opin Microbiol 2021; 63:1-9. [PMID: 34098411 PMCID: PMC8525121 DOI: 10.1016/j.mib.2021.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/16/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022]
Abstract
Bacterial microcompartments (BMCs) are self-assembling prokaryotic organelles which encapsulate enzymes within a polyhedral protein shell. The shells are comprised of only two structural modules, distinct domains that form pentagonal and hexagonal building blocks, which occupy the vertices and facets, respectively. As all BMC loci encode at least one hexamer-forming and one pentamer-forming protein, the evolutionary history of BMCs can be interrogated from the perspective of their shells. Here, we discuss how structures of intact shells and detailed phylogenies of their building blocks from a recent phylogenomic survey distinguish families of these domains and reveal clade-specific structural features. These features suggest distinct functional roles that recur across diverse BMCs. For example, it is clear that carboxysomes independently arose twice from metabolosomes, yet the principles of shell assembly are remarkably conserved.
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Affiliation(s)
- Matthew R Melnicki
- Michigan State University-U.S. Department of Energy (MSU-DOE) Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Markus Sutter
- Michigan State University-U.S. Department of Energy (MSU-DOE) Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology Division and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Cheryl A Kerfeld
- Michigan State University-U.S. Department of Energy (MSU-DOE) Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology Division and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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17
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Bobik TA, Stewart AM. Selective molecular transport across the protein shells of bacterial microcompartments. Curr Opin Microbiol 2021; 62:76-83. [PMID: 34087617 PMCID: PMC8286307 DOI: 10.1016/j.mib.2021.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/20/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022]
Abstract
Bacterial microcompartments are widespread organelles that play important roles in the environment and are associated with a number of human diseases. A key feature of bacterial MCPs is a selectively permeable protein shell that mediates the movement of substrates, products and cofactors in and out. Here we discuss current knowledge of selective transport across the protein shells of bacterial MCPs, including mechanisms, regulation and unanswered questions.
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Affiliation(s)
- Thomas A Bobik
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - Andrew M Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Sutter M, Melnicki MR, Schulz F, Woyke T, Kerfeld CA. A catalog of the diversity and ubiquity of bacterial microcompartments. Nat Commun 2021; 12:3809. [PMID: 34155212 PMCID: PMC8217296 DOI: 10.1038/s41467-021-24126-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/28/2021] [Indexed: 12/25/2022] Open
Abstract
Bacterial microcompartments (BMCs) are organelles that segregate segments of metabolic pathways which are incompatible with surrounding metabolism. BMCs consist of a selectively permeable shell, composed of three types of structurally conserved proteins, together with sequestered enzymes that vary among functionally distinct BMCs. Genes encoding shell proteins are typically clustered with those for the encapsulated enzymes. Here, we report that the number of identifiable BMC loci has increased twenty-fold since the last comprehensive census of 2014, and the number of distinct BMC types has doubled. The new BMC types expand the range of compartmentalized catalysis and suggest that there is more BMC biochemistry yet to be discovered. Our comprehensive catalog of BMCs provides a framework for their identification, correlation with bacterial niche adaptation, experimental characterization, and development of BMC-based nanoarchitectures for biomedical and bioengineering applications. Bacterial microcompartments (BMCs) are organelles consisting of a protein shell in which certain metabolic reactions take place separated from the cytoplasm. Here, Sutter et al. present a comprehensive catalog of BMC loci, substantially expanding the number of known BMCs and describing distinct types and compartmentalized reactions.
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Affiliation(s)
- Markus Sutter
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Matthew R Melnicki
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cheryl A Kerfeld
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA. .,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Ochoa JM, Yeates TO. Recent structural insights into bacterial microcompartment shells. Curr Opin Microbiol 2021; 62:51-60. [PMID: 34058518 DOI: 10.1016/j.mib.2021.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/26/2021] [Accepted: 04/20/2021] [Indexed: 02/05/2023]
Abstract
Bacterial microcompartments are organelle-like structures that enhance a variety of metabolic functions in diverse bacteria. Composed entirely of proteins, thousands of homologous hexameric shell proteins tesselate to form facets while pentameric proteins form the vertices of a polyhedral shell that encapsulates various enzymes, substrates and cofactors. Recent structural data have highlighted nuanced variations in the sequence and topology of microcompartment shell proteins, emphasizing how variation and specialization enable the construction of complex molecular machines. Recent studies engineering synthetic miniaturized microcompartment shells provide additional frameworks for dissecting principles of microcompartment structure and assembly. This review updates our current understanding of bacterial microcompartment shell proteins, providing new insights and highlighting outstanding questions.
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Cesle EE, Filimonenko A, Tars K, Kalnins G. Variety of size and form of GRM2 bacterial microcompartment particles. Protein Sci 2021; 30:1035-1043. [PMID: 33763934 PMCID: PMC8040866 DOI: 10.1002/pro.4069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022]
Abstract
Bacterial microcompartments (BMCs) are bacterial organelles involved in enzymatic processes, such as carbon fixation, choline, ethanolamine and propanediol degradation, and others. Formed of a semi-permeable protein shell and an enzymatic core, they can enhance enzyme performance and protect the cell from harmful intermediates. With the ability to encapsulate non-native enzymes, BMCs show high potential for applied use. For this goal, a detailed look into shell form variability is significant to predict shell adaptability. Here we present four novel 3D cryo-EM maps of recombinant Klebsiella pneumoniae GRM2 BMC shell particles with the resolution in range of 9 to 22 Å and nine novel 2D classes corresponding to discrete BMC shell forms. These structures reveal icosahedral, elongated, oblate, multi-layered and polyhedral traits of BMCs, indicating considerable variation in size and form as well as adaptability during shell formation processes.
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Affiliation(s)
- Eva Emilija Cesle
- Structural Biology, Biotechnology and Virusology LaboratoryLatvian Biomedical Research and Study CentreRigaLatvia
| | - Anatolij Filimonenko
- CEITEC‐Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Kaspars Tars
- Structural Biology, Biotechnology and Virusology LaboratoryLatvian Biomedical Research and Study CentreRigaLatvia
- Faculty of BiologyUniversity of LatviaRigaLatvia
| | - Gints Kalnins
- Structural Biology, Biotechnology and Virusology LaboratoryLatvian Biomedical Research and Study CentreRigaLatvia
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24
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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25
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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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26
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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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27
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Podgorski J, Calabrese J, Alexandrescu L, Jacobs-Sera D, Pope W, Hatfull G, White S. Structures of Three Actinobacteriophage Capsids: Roles of Symmetry and Accessory Proteins. Viruses 2020; 12:v12030294. [PMID: 32182721 PMCID: PMC7150772 DOI: 10.3390/v12030294] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 02/07/2023] Open
Abstract
Here, we describe the structure of three actinobacteriophage capsids that infect Mycobacterium smegmatis. The capsid structures were resolved to approximately six angstroms, which allowed confirmation that each bacteriophage uses the HK97-fold to form their capsid. One bacteriophage, Rosebush, may have a novel variation of the HK97-fold. Four novel accessory proteins that form the capsid head along with the major capsid protein were identified. Two of the accessory proteins were minor capsid proteins and showed some homology, based on bioinformatic analysis, to the TW1 bacteriophage. The remaining two accessory proteins are decoration proteins that are located on the outside of the capsid and do not resemble any previously described bacteriophage decoration protein. SDS-PAGE and mass spectrometry was used to identify the accessory proteins and bioinformatic analysis of the accessory proteins suggest they are used in many actinobacteriophage capsids.
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Affiliation(s)
- Jennifer Podgorski
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125. Storrs, CT 06269-3125, USA; (J.P.); (J.C.); (L.A.)
| | - Joshua Calabrese
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125. Storrs, CT 06269-3125, USA; (J.P.); (J.C.); (L.A.)
| | - Lauren Alexandrescu
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125. Storrs, CT 06269-3125, USA; (J.P.); (J.C.); (L.A.)
| | - Deborah Jacobs-Sera
- Clapp Hall, Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA; (D.J.-S.); (W.P.); (G.H.)
| | - Welkin Pope
- Clapp Hall, Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA; (D.J.-S.); (W.P.); (G.H.)
| | - Graham Hatfull
- Clapp Hall, Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA; (D.J.-S.); (W.P.); (G.H.)
| | - Simon White
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125. Storrs, CT 06269-3125, USA; (J.P.); (J.C.); (L.A.)
- Correspondence:
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Chowdhury C, Bobik TA. Engineering the PduT shell protein to modify the permeability of the 1,2-propanediol microcompartment of Salmonella. Microbiology (Reading) 2020; 165:1355-1364. [PMID: 31674899 DOI: 10.1099/mic.0.000872] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacterial microcompartments (MCPs) are protein-based organelles that consist of metabolic enzymes encapsulated within a protein shell. The function of MCPs is to optimize metabolic pathways by increasing reaction rates and sequestering toxic pathway intermediates. A substantial amount of effort has been directed toward engineering synthetic MCPs as intracellular nanoreactors for the improved production of renewable chemicals. A key challenge in this area is engineering protein shells that allow the entry of desired substrates. In this study, we used site-directed mutagenesis of the PduT shell protein to remove its central iron-sulfur cluster and create openings (pores) in the shell of the Pdu MCP that have varied chemical properties. Subsequently, in vivo and in vitro studies were used to show that PduT-C38S and PduT-C38A variants increased the diffusion of 1,2-propanediol, propionaldehyde, NAD+ and NADH across the shell of the MCP. In contrast, PduT-C38I and PduT-C38W eliminated the iron-sulfur cluster without altering the permeability of the Pdu MCP, suggesting that the side-chains of C38I and C38W occluded the opening formed by removal of the iron-sulfur cluster. Thus, genetic modification offers an approach to engineering the movement of larger molecules (such as NAD/H) across MCP shells, as well as a method for blocking transport through trimeric bacterial microcompartment (BMC) domain shell proteins.
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Affiliation(s)
- Chiranjit Chowdhury
- Present address: Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Campus, Sector-125, Noida, UP-201313, India.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
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Huang J, Ferlez BH, Young EJ, Kerfeld CA, Kramer DM, Ducat DC. Functionalization of Bacterial Microcompartment Shell Proteins With Covalently Attached Heme. Front Bioeng Biotechnol 2020; 7:432. [PMID: 31993414 PMCID: PMC6962350 DOI: 10.3389/fbioe.2019.00432] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/05/2019] [Indexed: 12/26/2022] Open
Abstract
Heme is a versatile redox cofactor that has considerable potential for synthetic biology and bioelectronic applications. The capacity to functionalize non-heme-binding proteins with covalently bound heme moieties in vivo could expand the variety of bioelectronic materials, particularly if hemes could be attached at defined locations so as to facilitate position-sensitive processes like electron transfer. In this study, we utilized the cytochrome maturation system I to develop a simple approach that enables incorporation of hemes into the backbone of target proteins in vivo. We tested our methodology by targeting the self-assembling bacterial microcompartment shell proteins, and inserting functional hemes at multiple locations in the protein backbone. We found substitution of three amino acids on the target proteins promoted heme attachment with high occupancy. Spectroscopic measurements suggested these modified proteins covalently bind low-spin hemes, with relative low redox midpoint potentials (about -210 mV vs. SHE). Heme-modified shell proteins partially retained their self-assembly properties, including the capacity to hexamerize, and form inter-hexamer attachments. Heme-bound shell proteins demonstrated the capacity to integrate into higher-order shell assemblies, however, the structural features of these macromolecular complexes was sometimes altered. Altogether, we report a versatile strategy for generating electron-conductive cytochromes from structurally-defined proteins, and provide design considerations on how heme incorporation may interface with native assembly properties in engineered proteins.
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Affiliation(s)
- Jingcheng Huang
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Bryan H. Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Eric J. Young
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - David M. Kramer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Daniel C. Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
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Sutter M, Laughlin TG, Sloan NB, Serwas D, Davies KM, Kerfeld CA. Structure of a Synthetic β-Carboxysome Shell. Plant Physiol 2019; 181:1050-1058. [PMID: 31501298 PMCID: PMC6836842 DOI: 10.1104/pp.19.00885] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/24/2019] [Indexed: 05/30/2023]
Abstract
Carboxysomes are capsid-like, CO2-fixing organelles that are present in all cyanobacteria and some chemoautotrophs and that substantially contribute to global primary production. They are composed of a selectively permeable protein shell that encapsulates Rubisco, the principal CO2-fixing enzyme, and carbonic anhydrase. As the centerpiece of the carbon-concentrating mechanism, by packaging enzymes that collectively enhance catalysis, the carboxysome shell enables the generation of a locally elevated concentration of substrate CO2 and the prevention of CO2 escape. A functional carboxysome consisting of an intact shell and cargo is essential for cyanobacterial growth under ambient CO2 concentrations. Using cryo-electron microscopy, we have determined the structure of a recombinantly produced simplified β-carboxysome shell. The structure reveals the sidedness and the specific interactions between the carboxysome shell proteins. The model provides insight into the structural basis of selective permeability of the carboxysome shell and can be used to design modifications to investigate the mechanisms of cargo encapsulation and other physiochemical properties such as permeability. Notably, the permeability properties are of great interest for modeling and evaluating this carbon-concentrating mechanism in metabolic engineering. Moreover, we find striking similarity between the carboxysome shell and the structurally characterized, evolutionarily distant metabolosome shell, implying universal architectural principles for bacterial microcompartment shells.
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Affiliation(s)
- Markus Sutter
- Environmental Genomics and Systems Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Thomas G Laughlin
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Nancy B Sloan
- Environmental Genomics and Systems Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Daniel Serwas
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Karen M Davies
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Cheryl A Kerfeld
- Environmental Genomics and Systems Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Planamente S, Frank S. Bio-engineering of bacterial microcompartments: a mini review. Biochem Soc Trans 2019; 47:765-77. [DOI: 10.1042/bst20170564] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [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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