1
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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. ACS OMEGA 2024; 9:35503-35514. [PMID: 39184480 PMCID: PMC11339822 DOI: 10.1021/acsomega.4c02406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 08/27/2024]
Abstract
Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria that encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable 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 used 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 the 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, Michigan 48824, United States
| | - Daipayan Sarkar
- MSU-DOE
Plant Research Laboratory, Michigan State
University, East Lansing, Michigan 48824, United States
| | - Leanne Jade G. Chan
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Joshua Mae
- MSU-DOE
Plant Research Laboratory, Michigan State
University, East Lansing, Michigan 48824, United States
| | - Markus Sutter
- MSU-DOE
Plant Research Laboratory, Michigan State
University, East Lansing, Michigan 48824, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J. Petzold
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Cheryl A. Kerfeld
- MSU-DOE
Plant Research Laboratory, Michigan State
University, East Lansing, Michigan 48824, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| | - Corie Y. Ralston
- Molecular
Foundry Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Sayan Gupta
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Josh V. Vermaas
- MSU-DOE
Plant Research Laboratory, Michigan State
University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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2
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Doron L, Kerfeld CA. Bacterial microcompartments as a next-generation metabolic engineering tool: utilizing nature's solution for confining challenging catabolic pathways. Biochem Soc Trans 2024; 52:997-1010. [PMID: 38813858 PMCID: PMC11346464 DOI: 10.1042/bst20230229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Advancements in synthetic biology have facilitated the incorporation of heterologous metabolic pathways into various bacterial chassis, leading to the synthesis of targeted bioproducts. However, total output from heterologous production pathways can suffer from low flux, enzyme promiscuity, formation of toxic intermediates, or intermediate loss to competing reactions, which ultimately hinder their full potential. The self-assembling, easy-to-modify, protein-based bacterial microcompartments (BMCs) offer a sophisticated way to overcome these obstacles by acting as an autonomous catalytic module decoupled from the cell's regulatory and metabolic networks. More than a decade of fundamental research on various types of BMCs, particularly structural studies of shells and their self-assembly, the recruitment of enzymes to BMC shell scaffolds, and the involvement of ancillary proteins such as transporters, regulators, and activating enzymes in the integration of BMCs into the cell's metabolism, has significantly moved the field forward. These advances have enabled bioengineers to design synthetic multi-enzyme BMCs to promote ethanol or hydrogen production, increase cellular polyphosphate levels, and convert glycerol to propanediol or formate to pyruvate. These pioneering efforts demonstrate the enormous potential of synthetic BMCs to encapsulate non-native multi-enzyme biochemical pathways for the synthesis of high-value products.
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Affiliation(s)
- Lior Doron
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, U.S.A
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3
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Waltmann C, Shrestha A, Olvera de la Cruz M. Patterning of multicomponent elastic shells by gaussian curvature. Phys Rev E 2024; 109:054409. [PMID: 38907410 DOI: 10.1103/physreve.109.054409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/19/2024] [Indexed: 06/24/2024]
Abstract
Recent findings suggest that shell protein distribution and the morphology of bacterial microcompartments regulate the chemical fluxes facilitating reactions which dictate their biological function. We explore how the morphology and component patterning are coupled through the competition of mean and gaussian bending energies in multicomponent elastic shells that form three-component irregular polyhedra. We observe two softer components with lower bending rigidities allocated on the edges and vertices while the harder component occupies the faces. When subjected to a nonzero interfacial line tension, the two softer components further separate and pattern into subdomains that are mediated by the gaussian curvature. We find that this degree of fractionation is maximized when there is a weaker line tension and when the ratio of bending rigidities between the two softer domains ≈2. Our results reveal a patterning mechanism in multicomponent shells that can capture the observed morphologies of bacterial microcompartments, and moreover, can be realized in synthetic vesicles.
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Affiliation(s)
| | | | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
- Center for Computation and Theory of Soft Materials, Northwestern University, Evanston, Illinois 60208, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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4
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Abeysinghe AADT, Young EJ, Rowland AT, Dunshee LC, Urandur S, Sullivan MO, Kerfeld CA, Keating CD. Interfacial Assembly of Bacterial Microcompartment Shell Proteins in Aqueous Multiphase Systems. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308390. [PMID: 38037673 DOI: 10.1002/smll.202308390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/13/2023] [Indexed: 12/02/2023]
Abstract
Compartments are a fundamental feature of life, based variously on lipid membranes, protein shells, or biopolymer phase separation. Here, this combines self-assembling bacterial microcompartment (BMC) shell proteins and liquid-liquid phase separation (LLPS) to develop new forms of compartmentalization. It is found that BMC shell proteins assemble at the liquid-liquid interfaces between either 1) the dextran-rich droplets and PEG-rich continuous phase of a poly(ethyleneglycol)(PEG)/dextran aqueous two-phase system, or 2) the polypeptide-rich coacervate droplets and continuous dilute phase of a polylysine/polyaspartate complex coacervate system. Interfacial protein assemblies in the coacervate system are sensitive to the ratio of cationic to anionic polypeptides, consistent with electrostatically-driven assembly. In both systems, interfacial protein assembly competes with aggregation, with protein concentration and polycation availability impacting coating. These two LLPS systems are then combined to form a three-phase system wherein coacervate droplets are contained within dextran-rich phase droplets. Interfacial localization of BMC hexameric shell proteins is tunable in a three-phase system by changing the polyelectrolyte charge ratio. The tens-of-micron scale BMC shell protein-coated droplets introduced here can accommodate bioactive cargo such as enzymes or RNA and represent a new synthetic cell strategy for organizing biomimetic functionality.
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Affiliation(s)
| | - Eric J Young
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Andrew T Rowland
- Department of Chemistry, Pennsylvania State University, State College, PA, 16801, USA
| | - Lucas C Dunshee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Sandeep Urandur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Cheryl A Kerfeld
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Christine D Keating
- Department of Chemistry, Pennsylvania State University, State College, PA, 16801, USA
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5
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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6
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Christians LF, Halingstad EV, Kram E, Okolovitch EM, Pak AJ. Formalizing Coarse-Grained Representations of Anisotropic Interactions at Multimeric Protein Interfaces Using Virtual Sites. J Phys Chem B 2024; 128:1394-1406. [PMID: 38316012 DOI: 10.1021/acs.jpcb.3c07023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Molecular simulations of biomacromolecules that assemble into multimeric complexes remain a challenge due to computationally inaccessible length and time scales. Low-resolution and implicit-solvent coarse-grained modeling approaches using traditional nonbonded interactions (both pairwise and spherically isotropic) have been able to partially address this gap. However, these models may fail to capture the complex anisotropic interactions present at macromolecular interfaces unless higher-order interaction potentials are incorporated at the expense of the computational cost. In this work, we introduce an alternate and systematic approach to represent directional interactions at protein-protein interfaces by using virtual sites restricted to pairwise interactions. We show that virtual site interaction parameters can be optimized within a relative entropy minimization framework by using only information from known statistics between coarse-grained sites. We compare our virtual site models to traditional coarse-grained models using two case studies of multimeric protein assemblies and find that the virtual site models predict pairwise correlations with higher fidelity and, more importantly, assembly behavior that is morphologically consistent with experiments. Our study underscores the importance of anisotropic interaction representations and paves the way for more accurate yet computationally efficient coarse-grained simulations of macromolecular assembly in future research.
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Affiliation(s)
- Luc F Christians
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Ethan V Halingstad
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Emiel Kram
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Evan M Okolovitch
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Alexander J Pak
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- Quantitative Biosciences and Engineering Program, Colorado School of Mines, Golden, Colorado 80401, United States
- Materials Science Program, Colorado School of Mines, Golden, Colorado 80401, United States
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7
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Shinde YD, Chowdhury C. Potential utility of bacterial protein nanoreactor for sustainable in-situ biocatalysis in wide range of bioprocess conditions. Enzyme Microb Technol 2024; 173:110354. [PMID: 37988973 DOI: 10.1016/j.enzmictec.2023.110354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/30/2023] [Accepted: 11/04/2023] [Indexed: 11/23/2023]
Abstract
Bacterial microcompartments (MCPs) are proteinaceous organelles that natively encapsulates the enzymes, substrates, and cofactors within a protein shell. They optimize the reaction rates by enriching the substrate in the vicinity of enzymes to increase the yields of the product and mitigate the outward diffusion of the toxic or volatile intermediates. The shell protein subunits of MCP shell are selectively permeable and have specialized pores for the selective inward diffusion of substrates and products release. Given their attributes, MCPs have been recently explored as potential candidates as subcellular nano-bioreactor for the enhanced production of industrially important molecules by exercising pathway encapsulation. In the current study, MCPs have been shown to sustain enzyme activity for extended periods, emphasizing their durability against a range of physical challenges such as temperature, pH and organic solvents. The significance of an intact shell in conferring maximum protection is highlighted by analyzing the differences in enzyme activities inside the intact and broken shell. Moreover, a minimal synthetic shell was designed with recruitment of a heterologous enzyme cargo to demonstrate the improved durability of the enzyme. The encapsulated enzyme was shown to be more stable than its free counterpart under the aforementioned conditions. Bacterial MCP-mediated encapsulation can serve as a potential strategy to shield the enzymes used under extreme conditions by maintaining the internal microenvironment and enhancing their cycle life, thereby opening new means for stabilizing, and reutilizing the enzymes in several bioprocess industries.
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Affiliation(s)
- Yashodhara D Shinde
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, MH 411008, India
| | - Chiranjit Chowdhury
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, MH 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP 201002, India.
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8
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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] [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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9
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Zhang Y, Kang R, Zhang X, Pang G, Li L, Han C, Liu B, Xue X, Liu J, Sun T, Wang T, Liu P, Wang H. A programmable oral bacterial hydrogel for controllable production and release of nanovaccine for tumor immunotherapy. Biomaterials 2023; 299:122147. [PMID: 37182418 DOI: 10.1016/j.biomaterials.2023.122147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/30/2023] [Accepted: 05/06/2023] [Indexed: 05/16/2023]
Abstract
Oral protein vaccines are mainly used to prevent the infection of intestinal pathogens in clinic due to their high safety and strong compliance. However, it is necessary to design the efficient delivery systems to overcome the harsh gastrointestinal environment in the application process. Here we established a programmable oral bacterial hydrogel system for spatiotemporally controllable production and release of nanovaccines. The system was divided into three parts: (1) Engineered bacteria were encapsulated in chitosan-sodium alginate microcapsules, which offered protection against the extreme acid conditions in the stomach. (2) Microcapsules were dissolved, and then engineered bacteria were released and colonized in the intestine. (3) The release of nanovaccines was controlled periodically by a synchronous lysis genetic circuit for tumor immunotherapy. Compared to control groups, tumor volume of subcutaneous tumor-bearing mice treated with bacterial microgels releasing optimized nanovaccine was almost inhibited by 75% and T cell response was activated at least 2-fold. We believe that this programmable bacterial hydrogel will offer a promising way for the application of oral nanovaccines.
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Affiliation(s)
- Yingying Zhang
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221006, China
| | - Ruru Kang
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Xinyu Zhang
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Gaoju Pang
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Lianyue Li
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Chunli Han
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Baona Liu
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Xin Xue
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Jing Liu
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Tao Sun
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, China; Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Tao Wang
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China
| | - Peiyuan Liu
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China.
| | - Hanjie Wang
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China.
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10
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Beal DM, Liang M, Brown I, Budge JD, Burrows ER, Howland K, Lee P, Martin S, Morrell A, Nemoto-Smith E, Roobol J, Stanley M, Smales CM, Warren MJ. Modification of bacterial microcompartments with target biomolecules via post-translational SpyTagging. MATERIALS ADVANCES 2023; 4:2963-2970. [PMID: 37465645 PMCID: PMC10350929 DOI: 10.1039/d3ma00071k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/31/2023] [Indexed: 07/20/2023]
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelle-like structures formed within bacteria, often encapsulating enzymes and cellular processes, in particular, allowing toxic intermediates to be shielded from the general cellular environment. Outside of their biological role they are of interest, through surface modification, as potential drug carriers and polyvalent antigen display scaffolds. Here we use a post-translational modification approach, using copper free click chemistry, to attach a SpyTag to a target protein molecule for attachment to a specific SpyCatcher modified BMC shell protein. We demonstrate that a post-translationally SpyTagged material can react with a SpyCatcher modified BMC and show its presence on the surface of BMCs, enabling future investigation of these structures as polyvalent antigen display scaffolds for vaccine development. This post-translational 'click' methodology overcomes the necessity to genetically encode the SpyTag, avoids any potential reduction in expression yield and expands the scope of SpyTag/SpyCatcher vaccine scaffolds to form peptide epitope vaccines and small molecule delivery agents.
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Affiliation(s)
- David M Beal
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Mingzhi Liang
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Ian Brown
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - James D Budge
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | | | - Kevin Howland
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Phoebe Lee
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | | | - Andrew Morrell
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | | | - Joanne Roobol
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Maria Stanley
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - C Mark Smales
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co Dublin A94 X099 Ireland
| | - Martin J Warren
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
- Quadram Institute Bioscience Norwich UK
- Norwich Medical School, University of East Anglia Norwich UK
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11
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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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12
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Raba DA, Kerfeld CA. The potential of bacterial microcompartment architectures for phytonanotechnology. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:700-710. [PMID: 35855583 DOI: 10.1111/1758-2229.13104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
The application of nanotechnology to plants, termed phytonanotechnology, has the potential to revolutionize plant research and agricultural production. Advancements in phytonanotechnology will allow for the time-controlled and target-specific release of bioactive compounds and agrochemicals to alter and optimize conventional plant production systems. A diverse range of engineered nanoparticles with unique physiochemical properties is currently being investigated to determine their suitability for plants. Improvements in crop yield, disease resistance and nutrient and pesticide management are all possible using designed nanocarriers. However, despite these prospective benefits, research to thoroughly understand the precise activity, localization and potential phytotoxicity of these nanoparticles within plant systems is required. Protein-based bacterial microcompartment shell proteins that self-assemble into spherical shells, nanotubes and sheets could be of immense value for phytonanotechnology due to their ease of manipulation, multifunctionality, rapid and efficient producibility and biodegradability. In this review, we explore bacterial microcompartment-based architectures within the scope of phytonanotechnology.
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Affiliation(s)
- Daniel A Raba
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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13
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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] [Key Words] [MESH Headings] [Grants] [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.
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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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14
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Tsidilkovski L, Mohajerani F, Hagan MF. Microcompartment assembly around multicomponent fluid cargoes. J Chem Phys 2022; 156:245104. [PMID: 35778087 PMCID: PMC9249432 DOI: 10.1063/5.0089556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This article describes dynamical simulations of the assembly of an icosahedral protein shell around a bicomponent fluid cargo. Our simulations are motivated by bacterial microcompartments, which are protein shells found in bacteria that assemble around a complex of enzymes and other components involved in certain metabolic processes. The simulations demonstrate that the relative interaction strengths among the different cargo species play a key role in determining the amount of each species that is encapsulated, their spatial organization, and the nature of the shell assembly pathways. However, the shell protein–shell protein and shell protein–cargo component interactions that help drive assembly and encapsulation also influence cargo composition within certain parameter regimes. These behaviors are governed by a combination of thermodynamic and kinetic effects. In addition to elucidating how natural microcompartments encapsulate multiple components involved within reaction cascades, these results have implications for efforts in synthetic biology to colocalize alternative sets of molecules within microcompartments to accelerate specific reactions. More broadly, the results suggest that coupling between self-assembly and multicomponent liquid–liquid phase separation may play a role in the organization of the cellular cytoplasm.
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Affiliation(s)
- Lev Tsidilkovski
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
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15
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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: 45] [Impact Index Per Article: 22.5] [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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16
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Abstract
Carboxysomes are anabolic bacterial microcompartments that play an essential role in carbon fixation in cyanobacteria and some chemoautotrophs. This self-assembling organelle encapsulates the key CO2-fixing enzymes, Rubisco, and carbonic anhydrase using a polyhedral protein shell that is constructed by hundreds of shell protein paralogs. The α-carboxysome from the chemoautotroph Halothiobacillus neapolitanus serves as a model system in fundamental studies and synthetic engineering of carboxysomes. In this study, we adopted a QconCAT-based quantitative mass spectrometry approach to determine the stoichiometric composition of native α-carboxysomes from H. neapolitanus. We further performed an in-depth comparison of the protein stoichiometry of native α-carboxysomes and their recombinant counterparts heterologously generated in Escherichia coli to evaluate the structural variability and remodeling of α-carboxysomes. Our results provide insight into the molecular principles that mediate carboxysome assembly, which may aid in rational design and reprogramming of carboxysomes in new contexts for biotechnological applications. IMPORTANCE A wide range of bacteria use special protein-based organelles, termed bacterial microcompartments, to encase enzymes and reactions to increase the efficiency of biological processes. As a model bacterial microcompartment, the carboxysome contains a protein shell filled with the primary carbon fixation enzyme Rubisco. The self-assembling organelle is generated by hundreds of proteins and plays important roles in converting carbon dioxide to sugar, a process known as carbon fixation. In this study, we uncovered the exact stoichiometry of all building components and the structural plasticity of the functional α-carboxysome, using newly developed quantitative mass spectrometry together with biochemistry, electron microscopy, and enzymatic assay. The study advances our understanding of the architecture and modularity of natural carboxysomes. The knowledge learned from natural carboxysomes will suggest feasible ways to produce functional carboxysomes in other hosts, such as crop plants, with the overwhelming goal of boosting cell metabolism and crop yields.
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17
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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: 22] [Impact Index Per Article: 11.0] [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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18
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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] [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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19
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Li S, Matoz-Fernandez DA, Olvera de la Cruz M. Effect of Mechanical Properties on Multicomponent Shell Patterning. ACS NANO 2021; 15:14804-14812. [PMID: 34402621 DOI: 10.1021/acsnano.1c04795] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Self-organized shells are fundamental in biological compartmentalization. They protect genomic material or enclose enzymes to aid the metabolic process. Studies of crystalline shells have shown the importance of the mechanical properties of building units in the shell morphology. However, the mechanism underlying the morphology of multicomponent assemblies is still poorly understood. Here, we analyze multicomponent closed shells that have different mechanical properties. By minimizing elastic energy, we show that heterogeneous bending rigidities regulate the surface pattern into circular, spikes, and ridge shapes. Interestingly, our continuum elasticity model recovers the patterns that have been proposed in bacterial microcompartments (BMCs), which are self-organized protein shells that aid the breakdown of complex molecules and allow bacteria to survive in hostile environments. In addition, our work elucidates the principles of pattern formation that can be used to design and engineer multicomponent microcompartments with a specific surface distribution of the components.
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Affiliation(s)
- Siyu Li
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, United States
| | - Daniel A Matoz-Fernandez
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Physics and Astronomy, 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 Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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20
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Tan YQ, Ali S, Xue B, Teo WZ, Ling LH, Go MK, Lv H, Robinson RC, Narita A, Yew WS. Structure of a Minimal α-Carboxysome-Derived Shell and Its Utility in Enzyme Stabilization. Biomacromolecules 2021; 22:4095-4109. [PMID: 34384019 DOI: 10.1021/acs.biomac.1c00533] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bacterial microcompartments are proteinaceous shells that encase specialized metabolic processes in bacteria. Recent advances in simplification of these intricate shells have encouraged bioengineering efforts. Here, we construct minimal shells derived from the Halothiobacillus neapolitanus α-carboxysome, which we term Cso-shell. Using cryogenic electron microscopy, the atomic-level structures of two shell forms were obtained, reinforcing notions of evolutionarily conserved features in bacterial microcompartment shell architecture. Encapsulation peptide sequences that facilitate loading of heterologous protein cargo within the shells were identified. We further provide a first demonstration in utilizing minimal bacterial microcompartment-derived shells for hosting heterologous enzymes. Cso-shells were found to stabilize enzymatic activities against heat shock, presence of methanol co-solvent, consecutive freeze-thawing, and alkaline environments. This study yields insights into α-carboxysome assembly and advances the utility of synthetic bacterial microcompartments as nanoreactors capable of stabilizing enzymes with varied properties and reaction chemistries.
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Affiliation(s)
- Yong Quan Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Graduate School for Integrative Sciences and Engineering, NUS, Singapore 119077
| | - Samson Ali
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Research Institute for Interdisciplinary Science (RIIS), Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Bo Xue
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Wei Zhe Teo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Lay Hiang Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Graduate School for Integrative Sciences and Engineering, NUS, Singapore 119077
| | - Maybelle Kho Go
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Hong Lv
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, People's Republic of China.,State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200438, People's Republic of China
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Akihiro Narita
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Graduate School for Integrative Sciences and Engineering, NUS, Singapore 119077.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
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21
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Kumar G, Sinha S. Biophysical approaches to understand and re-purpose bacterial microcompartments. Curr Opin Microbiol 2021; 63:43-51. [PMID: 34166983 DOI: 10.1016/j.mib.2021.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/15/2021] [Accepted: 05/17/2021] [Indexed: 11/30/2022]
Abstract
Bacterial microcompartments represent a modular class of prokaryotic organelles associated with metabolic processes. They harbor a congregation of enzymes that work in cascade within a small, confined volume. These sophisticated nano-engineered crafts of nature offer a tempting paradigm for the fabrication of biosynthetic nanoreactors. Repurposing bacterial microcompartments to develop nanostructures with desired functions requires a careful manipulation in their structural makeup and composition. This calls for a comprehensive understanding of all the interactions of the physical components which frame such molecular architectures. Over recent years, several biophysical techniques have been essential in illuminating the role played by bacterial microcompartments within cells, and have revealed crucial details regarding the morphology, physical properties and functions of their constituent proteins. This has promoted contemplation of ideas for engineering microcompartments inspired biomaterials with novel features and functions.
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Affiliation(s)
- Gaurav Kumar
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector-81, Mohali (SAS Nagar), Knowledge City, Punjab 140306, India
| | - Sharmistha Sinha
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector-81, Mohali (SAS Nagar), Knowledge City, Punjab 140306, India.
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22
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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: 21] [Impact Index Per Article: 7.0] [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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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] [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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Mohajerani F, Sayer E, Neil C, Inlow K, Hagan MF. Mechanisms of Scaffold-Mediated Microcompartment Assembly and Size Control. ACS NANO 2021; 15:4197-4212. [PMID: 33683101 PMCID: PMC8058603 DOI: 10.1021/acsnano.0c05715] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This article describes a theoretical and computational study of the dynamical assembly of a protein shell around a complex consisting of many cargo molecules and long, flexible scaffold molecules. Our study is motivated by bacterial microcompartments, which are proteinaceous organelles that assemble around a condensed droplet of enzymes and reactants. As in many examples of cytoplasmic liquid-liquid phase separation, condensation of the microcompartment interior cargo is driven by flexible scaffold proteins that have weak multivalent interactions with the cargo. Our results predict that the shell size, amount of encapsulated cargo, and assembly pathways depend sensitively on properties of the scaffold, including its length and valency of scaffold-cargo interactions. Moreover, the ability of self-assembling protein shells to change their size to accommodate scaffold molecules of different lengths depends crucially on whether the spontaneous curvature radius of the protein shell is smaller or larger than a characteristic elastic length scale of the shell. Beyond natural microcompartments, these results have important implications for synthetic biology efforts to target alternative molecules for encapsulation by microcompartments or viral shells. More broadly, the results elucidate how cells exploit coupling between self-assembly and liquid-liquid phase separation to organize their interiors.
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Affiliation(s)
- Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Evan Sayer
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Christopher Neil
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Koe Inlow
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
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25
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Groaz A, Moghimianavval H, Tavella F, Giessen TW, Vecchiarelli AG, Yang Q, Liu AP. Engineering spatiotemporal organization and dynamics in synthetic cells. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 13:e1685. [PMID: 33219745 DOI: 10.1002/wnan.1685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/13/2020] [Accepted: 10/30/2020] [Indexed: 12/28/2022]
Abstract
Constructing synthetic cells has recently become an appealing area of research. Decades of research in biochemistry and cell biology have amassed detailed part lists of components involved in various cellular processes. Nevertheless, recreating any cellular process in vitro in cell-sized compartments remains ambitious and challenging. Two broad features or principles are key to the development of synthetic cells-compartmentalization and self-organization/spatiotemporal dynamics. In this review article, we discuss the current state of the art and research trends in the engineering of synthetic cell membranes, development of internal compartmentalization, reconstitution of self-organizing dynamics, and integration of activities across scales of space and time. We also identify some research areas that could play a major role in advancing the impact and utility of engineered synthetic cells. This article is categorized under: Biology-Inspired Nanomaterials > Lipid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
| | | | | | | | | | - Qiong Yang
- University of Michigan, Ann Arbor, Michigan, USA
| | - Allen P Liu
- University of Michigan, Ann Arbor, Michigan, USA
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26
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Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein. Sci Rep 2020; 10:17501. [PMID: 33060756 PMCID: PMC7562746 DOI: 10.1038/s41598-020-74536-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/29/2020] [Indexed: 12/31/2022] Open
Abstract
Bacterial microcompartments (BMCs) are nanoscale proteinaceous organelles that encapsulate enzymes from the cytoplasm using an icosahedral protein shell that resembles viral capsids. Of particular interest are the carboxysomes (CBs), which sequester the CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to enhance carbon assimilation. The carboxysome shell serves as a semi-permeable barrier for passage of metabolites in and out of the carboxysome to enhance CO2 fixation. How the protein shell directs influx and efflux of molecules in an effective manner has remained elusive. Here we use molecular dynamics and umbrella sampling calculations to determine the free-energy profiles of the metabolic substrates, bicarbonate, CO2 and ribulose bisphosphate and the product 3-phosphoglycerate associated with their transition through the major carboxysome shell protein CcmK2. We elucidate the electrostatic charge-based permeability and key amino acid residues of CcmK2 functioning in mediating molecular transit through the central pore. Conformational changes of the loops forming the central pore may also be required for transit of specific metabolites. The importance of these in-silico findings is validated experimentally by site-directed mutagenesis of the key CcmK2 residue Serine 39. This study provides insight into the mechanism that mediates molecular transport through the shells of carboxysomes, applicable to other BMCs. It also offers a predictive approach to investigate and manipulate the shell permeability, with the intent of engineering BMC-based metabolic modules for new functions in synthetic biology.
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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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28
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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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29
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Lv X, Cui S, Gu Y, Li J, Du G, Liu L. Enzyme Assembly for Compartmentalized Metabolic Flux Control. Metabolites 2020; 10:E125. [PMID: 32224973 PMCID: PMC7241084 DOI: 10.3390/metabo10040125] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 11/16/2022] Open
Abstract
Enzyme assembly by ligand binding or physically sequestrating enzymes, substrates, or metabolites into isolated compartments can bring key molecules closer to enhance the flux of a metabolic pathway. The emergence of enzyme assembly has provided both opportunities and challenges for metabolic engineering. At present, with the development of synthetic biology and systems biology, a variety of enzyme assembly strategies have been proposed, from the initial direct enzyme fusion to scaffold-free assembly, as well as artificial scaffolds, such as nucleic acid/protein scaffolds, and even some more complex physical compartments. These assembly strategies have been explored and applied to the synthesis of various important bio-based products, and have achieved different degrees of success. Despite some achievements, enzyme assembly, especially in vivo, still has many problems that have attracted significant attention from researchers. Here, we focus on some selected examples to review recent research on scaffold-free strategies, synthetic artificial scaffolds, and physical compartments for enzyme assembly or pathway sequestration, and we discuss their notable advances. In addition, the potential applications and challenges in the applications are highlighted.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Shixiu Cui
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yang Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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30
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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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31
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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-SGM 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] [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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32
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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] [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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33
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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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34
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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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35
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Zhang G, Johnston T, Quin MB, Schmidt-Dannert C. Developing a Protein Scaffolding System for Rapid Enzyme Immobilization and Optimization of Enzyme Functions for Biocatalysis. ACS Synth Biol 2019; 8:1867-1876. [PMID: 31305981 DOI: 10.1021/acssynbio.9b00187] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Immobilization of enzymes is required for most biocatalytic processes, but chemistries used in enzyme immobilization are limited and can be challenging. Genetically encoded protein-based biomaterials could provide easy-to-use immobilization platforms for biocatalysts. We recently developed a self-assembling protein scaffold that covalently immobilized SpyTagged enzymes by engineering the bacterial microcompartment protein EutM from Salmonella enterica with a SpyCatcher domain. We also identified a range of EutM homologues as robust protein nanostructures with diverse architectures and electrostatic surface properties. In this work, we created a modular immobilization platform with tunable surface properties by developing a toolbox of self-assembling, robust EutM-SpyCatcher scaffolds. Using an alcohol dehydrogenase as model biocatalyst, we show that the scaffolds improve enzyme activity and stability. This work provides a modular, easy-to-use immobilization system that can be tailored for the optimal function of biocatalysts of interest.
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Affiliation(s)
- Guoqiang Zhang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Timothy Johnston
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Maureen B. Quin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, United States
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36
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Ferlez B, Sutter M, Kerfeld CA. A designed bacterial microcompartment shell with tunable composition and precision cargo loading. Metab Eng 2019; 54:286-291. [PMID: 31075444 PMCID: PMC6884132 DOI: 10.1016/j.ymben.2019.04.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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Affiliation(s)
- Bryan Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 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; Department of Biochemistry and Molecular Biology, Michigan State University, 603 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.
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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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Sutter M, McGuire S, Ferlez B, Kerfeld CA. Structural Characterization of a Synthetic Tandem-Domain Bacterial Microcompartment Shell Protein Capable of Forming Icosahedral Shell Assemblies. ACS Synth Biol 2019; 8:668-674. [PMID: 30901520 DOI: 10.1021/acssynbio.9b00011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial microcompartments are subcellular compartments found in many prokaryotes; they consist of a protein shell that encapsulates enzymes that perform a variety of functions. The shell protects the cell from potentially toxic intermediates and colocalizes enzymes for higher efficiency. Accordingly, it is of considerable interest for biotechnological applications. We have previously structurally characterized an intact 40 nm shell comprising three different types of proteins. One of those proteins, BMC-H, forms a cyclic hexamer; here we have engineered a synthetic protein that consists of a tandem duplication of BMC-H connected by a short linker. The synthetic protein forms cyclic trimers that self-assemble to form a smaller (25 nm) icosahedral shell with gaps at the pentamer positions. When coexpressed in vivo with the pentamer fused to an affinity tag we can purify complete icosahedral shells. This engineered shell protein constitutes a minimal shell system to study permeability; reducing symmetry from 6- to 3-fold will allow for finer control of the pore environment. We have determined a crystal structure of this shell to guide rational engineering of this microcompartment shell for biotechnological applications.
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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, California 94720, United States
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
| | - Sean McGuire
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Bryan Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Cheryl A. Kerfeld
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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Greber BJ, Sutter M, Kerfeld CA. The Plasticity of Molecular Interactions Governs Bacterial Microcompartment Shell Assembly. Structure 2019; 27:749-763.e4. [PMID: 30833088 DOI: 10.1016/j.str.2019.01.017] [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] [Received: 10/04/2018] [Revised: 11/07/2018] [Accepted: 01/28/2019] [Indexed: 12/30/2022]
Abstract
Bacterial microcompartments (BMCs) are composed of an enzymatic core encapsulated by a selectively permeable protein shell that enhances catalytic efficiency. Many pathogenic bacteria derive competitive advantages from their BMC-based catabolism, implicating BMCs as drug targets. BMC shells are of interest for bioengineering due to their diverse and selective permeability properties and because they self-assemble. A complete understanding of shell composition and organization is a prerequisite for biotechnological applications. Here, we report the cryoelectron microscopy structure of a BMC shell at 3.0-Å resolution, using an image-processing strategy that allowed us to determine the previously uncharacterized structural details of the interactions formed by the BMC-TS and BMC-TD shell subunits in the context of the assembled shell. We found unexpected structural plasticity among these interactions, resulting in distinct shell populations assembled from varying numbers of the BMC-TS and BMC-TD subunits. We discuss the implications of these findings on shell assembly and function.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Markus Sutter
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Cheryl A Kerfeld
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; 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, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Faulkner M, Zhao LS, Barrett S, Liu LN. Self-Assembly Stability and Variability of Bacterial Microcompartment Shell Proteins in Response to the Environmental Change. NANOSCALE RESEARCH LETTERS 2019; 14:54. [PMID: 30747342 PMCID: PMC6372710 DOI: 10.1186/s11671-019-2884-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/31/2019] [Indexed: 05/04/2023]
Abstract
Bacterial microcompartments (BMCs) are proteinaceous self-assembling organelles that are widespread among the prokaryotic kingdom. By segmenting key metabolic enzymes and pathways using a polyhedral shell, BMCs play essential roles in carbon assimilation, pathogenesis, and microbial ecology. The BMC shell is composed of multiple protein homologs that self-assemble to form the defined architecture. There is tremendous interest in engineering BMCs to develop new nanobioreactors and molecular scaffolds. Here, we report the quantitative characterization of the formation and self-assembly dynamics of BMC shell proteins under varying pH and salt conditions using high-speed atomic force microscopy (HS-AFM). We show that 400-mM salt concentration is prone to result in larger single-layered shell patches formed by shell hexamers, and a higher dynamic rate of hexamer self-assembly was observed at neutral pH. We also visualize the variability of shell proteins from hexameric assemblies to fiber-like arrays. This study advances our knowledge about the stability and variability of BMC protein self-assemblies in response to microenvironmental changes, which will inform rational design and construction of synthetic BMC structures with the capacity of remodeling their self-assembly and structural robustness. It also offers a powerful toolbox for quantitatively assessing the self-assembly and formation of BMC-based nanostructures in biotechnology applications.
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Affiliation(s)
- Matthew Faulkner
- Institute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK
| | - Long-Sheng Zhao
- Institute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK
| | - Steve Barrett
- Department of Physics, University of Liverpool, L69 7ZE, Liverpool, UK
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK
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Hagen AR, Plegaria JS, Sloan N, Ferlez B, Aussignargues C, Kerfeld CA. In Vitro Assembly of Diverse Bacterial Microcompartment Shell Architectures. NANO LETTERS 2018; 18:7030-7037. [PMID: 30346795 PMCID: PMC6309364 DOI: 10.1021/acs.nanolett.8b02991] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Bacterial microcompartments (BMCs) are organelles composed of a selectively permeable protein shell that encapsulates enzymes involved in CO2 fixation (carboxysomes) or carbon catabolism (metabolosomes). Confinement of sequential reactions by the BMC shell presumably increases the efficiency of the pathway by reducing the crosstalk of metabolites, release of toxic intermediates, and accumulation of inhibitory products. Because BMCs are composed entirely of protein and self-assemble, they are an emerging platform for engineering nanoreactors and molecular scaffolds. However, testing designs for assembly and function through in vivo expression is labor-intensive and has limited the potential of BMCs in bioengineering. Here, we developed a new method for in vitro assembly of defined nanoscale BMC architectures: shells and nanotubes. By inserting a "protecting group", a short ubiquitin-like modifier (SUMO) domain, self-assembly of shell proteins in vivo was thwarted, enabling preparation of concentrates of shell building blocks. Addition of the cognate protease removes the SUMO domain and subsequent mixing of the constituent shell proteins in vitro results in the self-assembly of three types of supramolecular architectures: a metabolosome shell, a carboxysome shell, and a BMC protein-based nanotube. We next applied our method to generate a metabolosome shell engineered with a hyper-basic luminal surface, allowing for the encapsulation of biotic or abiotic cargos functionalized with an acidic accessory group. This is the first demonstration of using charge complementarity to encapsulate diverse cargos in BMC shells. Collectively, our work provides a generally applicable method for in vitro assembly of natural and engineered BMC-based architectures.
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Affiliation(s)
- Andrew R. Hagen
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road Berkeley, CA 94720, USA
| | - Jefferson S. Plegaria
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Nancy Sloan
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road Berkeley, CA 94720, USA
| | - Bryan Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Clement Aussignargues
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Cheryl A. Kerfeld
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road Berkeley, CA 94720, USA
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA
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Liu Y, He X, Lim W, Mueller J, Lawrie J, Kramer L, Guo J, Niu W. Deciphering molecular details in the assembly of alpha-type carboxysome. Sci Rep 2018; 8:15062. [PMID: 30305640 PMCID: PMC6180065 DOI: 10.1038/s41598-018-33074-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 09/12/2018] [Indexed: 01/25/2023] Open
Abstract
Bacterial microcompartments (BMCs) are promising natural protein structures for applications that require the segregation of certain metabolic functions or molecular species in a defined microenvironment. To understand how endogenous cargos are packaged inside the protein shell is key for using BMCs as nano-scale reactors or delivery vesicles. In this report, we studied the encapsulation of RuBisCO into the α-type carboxysome from Halothiobacillus neapolitan. Our experimental data revealed that the CsoS2 scaffold proteins engage RuBisCO enzyme through an interaction with the small subunit (CbbS). In addition, the N domain of the large subunit (CbbL) of RuBisCO interacts with all shell proteins that can form the hexamers. The binding affinity between the N domain of CbbL and one of the major shell proteins, CsoS1C, is within the submicromolar range. The absence of the N domain also prevented the encapsulation of the rest of the RuBisCO subunits. Our findings complete the picture of how RuBisCOs are encapsulated into the α-type carboxysome and provide insights for future studies and engineering of carboxysome as a protein shell.
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Affiliation(s)
- Yilan Liu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Xinyuan He
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Weiping Lim
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Joshua Mueller
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Justin Lawrie
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Levi Kramer
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States.
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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: 34] [Impact Index Per Article: 5.7] [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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44
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Hagen A, Sutter M, Sloan N, Kerfeld CA. Programmed loading and rapid purification of engineered bacterial microcompartment shells. Nat Commun 2018; 9:2881. [PMID: 30038362 PMCID: PMC6056538 DOI: 10.1038/s41467-018-05162-z] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/15/2018] [Indexed: 12/30/2022] Open
Abstract
Bacterial microcompartments (BMCs) are selectively permeable proteinaceous organelles which encapsulate segments of metabolic pathways across bacterial phyla. They consist of an enzymatic core surrounded by a protein shell composed of multiple distinct proteins. Despite great potential in varied biotechnological applications, engineering efforts have been stymied by difficulties in their isolation and characterization and a dearth of robust methods for programming cores and shell permeability. We address these challenges by functionalizing shell proteins with affinity handles, enabling facile complementation-based affinity purification (CAP) and specific cargo docking sites for efficient encapsulation via covalent-linkage (EnCo). These shell functionalizations extend our knowledge of BMC architectural principles and enable the development of minimal shell systems of precisely defined structure and composition. The generalizability of CAP and EnCo will enable their application to functionally diverse microcompartment systems to facilitate both characterization of natural functions and the development of bespoke shells for selectively compartmentalizing proteins.
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Affiliation(s)
- Andrew Hagen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Markus Sutter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Nancy Sloan
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Cheryl A Kerfeld
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA. .,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA. .,Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI, 48824, USA.
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45
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Mohajerani F, Hagan MF. The role of the encapsulated cargo in microcompartment assembly. PLoS Comput Biol 2018; 14:e1006351. [PMID: 30063715 PMCID: PMC6086489 DOI: 10.1371/journal.pcbi.1006351] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/10/2018] [Accepted: 07/10/2018] [Indexed: 11/19/2022] Open
Abstract
Bacterial microcompartments are large, roughly icosahedral shells that assemble around enzymes and reactants involved in certain metabolic pathways in bacteria. Motivated by microcompartment assembly, we use coarse-grained computational and theoretical modeling to study the factors that control the size and morphology of a protein shell assembling around hundreds to thousands of molecules. We perform dynamical simulations of shell assembly in the presence and absence of cargo over a range of interaction strengths, subunit and cargo stoichiometries, and the shell spontaneous curvature. Depending on these parameters, we find that the presence of a cargo can either increase or decrease the size of a shell relative to its intrinsic spontaneous curvature, as seen in recent experiments. These features are controlled by a balance of kinetic and thermodynamic effects, and the shell size is assembly pathway dependent. We discuss implications of these results for synthetic biology efforts to target new enzymes to microcompartment interiors.
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Affiliation(s)
- Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
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46
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Abstract
Cyanobacteria sequester photosynthetic enzymes into microcompartments which facilitate the conversion of carbon dioxide into sugars. Geometric similarities between these structures and self-assembling viral capsids have inspired models that posit microcompartments as stable equilibrium arrangements of the constituent proteins. Here we describe a different mechanism for microcompartment assembly, one that is fundamentally nonequilibrium and yet highly reliable. This pathway is revealed by simulations of a molecular model resolving the size and shape of a cargo droplet and the extent and topography of an elastic shell. The resulting metastable microcompartment structures closely resemble those of carboxysomes, with a narrow size distribution and faceted shells. The essence of their assembly dynamics can be understood from a simpler mathematical model that combines elements of classical nucleation theory with continuum elasticity. These results highlight important control variables for achieving nanoscale encapsulation in general and for modulating the size and shape of carboxysomes in particular.
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47
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Plegaria JS, Kerfeld CA. Engineering nanoreactors using bacterial microcompartment architectures. Curr Opin Biotechnol 2018; 51:1-7. [PMID: 29035760 PMCID: PMC5899066 DOI: 10.1016/j.copbio.2017.09.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/19/2017] [Indexed: 12/30/2022]
Abstract
Bacterial microcompartments (BMCs) are organelles that encapsulate enzymes involved in CO2 fixation or carbon catabolism in a selectively permeable protein shell. Here, we highlight recent advances in the bioengineering of these protein-based nanoreactors in heterologous systems, including transfer and expression of BMC gene clusters, the production of template empty shells, and the encapsulation of non-native enzymes.
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Affiliation(s)
- Jefferson S Plegaria
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Berkeley Synthetic Biology Institute, Berkeley, CA 94720, USA.
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Abstract
Bacterial microcompartments (BMCs) are self-assembling organelles that consist of an enzymatic core that is encapsulated by a selectively permeable protein shell. The potential to form BMCs is widespread and found across the kingdom Bacteria. BMCs have crucial roles in carbon dioxide fixation in autotrophs and the catabolism of organic substrates in heterotrophs. They contribute to the metabolic versatility of bacteria, providing a competitive advantage in specific environmental niches. Although BMCs were first visualized more than 60 years ago, it is mainly in the past decade that progress has been made in understanding their metabolic diversity and the structural basis of their assembly and function. This progress has not only heightened our understanding of their role in microbial metabolism but is also beginning to enable their use in a variety of applications in synthetic biology. In this Review, we focus on recent insights into the structure, assembly, diversity and function of BMCs.
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Affiliation(s)
- Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Clement Aussignargues
- 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
| | - Jan Zarzycki
- Max-Planck-Institute for Terrestrial Microbiology, D-35043, Marburg, Germany
| | - Fei Cai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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A Bacterial Microcompartment Is Used for Choline Fermentation by Escherichia coli 536. J Bacteriol 2018; 200:JB.00764-17. [PMID: 29507086 DOI: 10.1128/jb.00764-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/23/2018] [Indexed: 01/16/2023] Open
Abstract
Bacterial choline degradation in the human gut has been associated with cancer and heart disease. In addition, recent studies found that a bacterial microcompartment is involved in choline utilization by Proteus and Desulfovibrio species. However, many aspects of this process have not been fully defined. Here, we investigate choline degradation by the uropathogen Escherichia coli 536. Growth studies indicated E. coli 536 degrades choline primarily by fermentation. Electron microscopy indicated that a bacterial microcompartment was used for this process. Bioinformatic analyses suggested that the choline utilization (cut) gene cluster of E. coli 536 includes two operons, one containing three genes and a main operon of 13 genes. Regulatory studies indicate that the cutX gene encodes a positive transcriptional regulator required for induction of the main cut operon in response to choline supplementation. Each of the 16 genes in the cut cluster was individually deleted, and phenotypes were examined. The cutX, cutY, cutF, cutO, cutC, cutD, cutU, and cutV genes were required for choline degradation, but the remaining genes of the cut cluster were not essential under the conditions used. The reasons for these varied phenotypes are discussed.IMPORTANCE Here, we investigate choline degradation in E. coli 536. These studies provide a basis for understanding a new type of bacterial microcompartment and may provide deeper insight into the link between choline degradation in the human gut and cancer and heart disease. These are also the first studies of choline degradation in E. coli 536, an organism for which sophisticated genetic analysis methods are available. In addition, the cut gene cluster of E. coli 536 is located in pathogenicity island II (PAI-II536) and hence might contribute to pathogenesis.
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50
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Kerfeld CA. A bioarchitectonic approach to the modular engineering of metabolism. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0387. [PMID: 28808103 DOI: 10.1098/rstb.2016.0387] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2017] [Indexed: 01/13/2023] Open
Abstract
Dissociating the complexity of metabolic processes into modules is a shift in focus from the single gene/gene product to functional and evolutionary units spanning the scale of biological organization. When viewing the levels of biological organization through this conceptual lens, modules are found across the continuum: domains within proteins, co-regulated groups of functionally associated genes, operons, metabolic pathways and (sub)cellular compartments. Combining modules as components or subsystems of a larger system typically leads to increased complexity and the emergence of new functions. By virtue of their potential for 'plug and play' into new contexts, modules can be viewed as units of both evolution and engineering. Through consideration of lessons learned from recent efforts to install new metabolic modules into cells and the emerging understanding of the structure, function and assembly of protein-based organelles, bacterial microcompartments, a structural bioengineering approach is described: one that builds from an architectural vocabulary of protein domains. This bioarchitectonic approach to engineering cellular metabolism can be applied to microbial cell factories, used in the programming of members of synthetic microbial communities or used to attain additional levels of metabolic organization in eukaryotic cells for increasing primary productivity and as the foundation of a green economy.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.
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Affiliation(s)
- Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA .,Molecular Biophysics and Integrated Bioimaging Division, 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.,Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA
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