1
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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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2
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Barthe L, Soldan V, Garcia-Alles LF. Assessment of oligomerization of bacterial micro-compartment shell components with the tripartite GFP reporter technology. PLoS One 2023; 18:e0294760. [PMID: 38011088 PMCID: PMC10681173 DOI: 10.1371/journal.pone.0294760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
Bacterial micro-compartments (BMC) are complex macromolecular assemblies that participate in varied metabolic processes in about 20% of bacterial species. Most of these organisms carry BMC genetic information organized in operons that often include several paralog genes coding for components of the compartment shell. BMC shell constituents can be classified depending on their oligomerization state as hexamers (BMC-H), pentamers (BMC-P) or trimers (BMC-T). Formation of hetero-oligomers combining different protein homologs is theoretically feasible, something that could ultimately modify BMC shell rigidity or permeability, for instance. Despite that, it remains largely unknown whether hetero-oligomerization is a widespread phenomenon. Here, we demonstrated that the tripartite GFP (tGFP) reporter technology is an appropriate tool that might be exploited for such purposes. Thus, after optimizing parameters such as the size of linkers connecting investigated proteins to GFP10 or GFP11 peptides, the type and strength of promoters, or the impact of placing coding cassettes in the same or different plasmids, homo-oligomerization processes could be successfully monitored for any of the three BMC shell classes. Moreover, the screen perfectly reproduced published data on hetero-association between couples of CcmK homologues from Syn. sp. PCC6803, which were obtained following a different approach. This study paves the way for mid/high throughput screens to characterize the extent of hetero-oligomerization occurrence in BMC-possessing bacteria, and most especially in organisms endowed with several BMC types and carrying numerous shell paralogs. On the other hand, our study also unveiled technology limitations deriving from the low solubility of one of the components of this modified split-GFP approach, the GFP1-9.
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Affiliation(s)
- Lucie Barthe
- Toulouse Biotechnology Institute, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
| | - Vanessa Soldan
- Plateforme de Microscopie Electronique Intégrative METi, CNRS, Centre de Biologie Intégrative, Toulouse, France
| | - Luis F. Garcia-Alles
- Toulouse Biotechnology Institute, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
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3
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Ochoa JM, Dershwitz P, Schappert M, Sinha S, Herring TI, Yeates TO, Bobik TA. A single shell protein plays a major role in choline transport across the shell of the choline utilization microcompartment of Escherichia coli 536. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001413. [PMID: 37971493 PMCID: PMC10710832 DOI: 10.1099/mic.0.001413] [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: 07/25/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
Bacterial microcompartments (MCPs) are widespread protein-based organelles that play important roles in the global carbon cycle and in the physiology of diverse bacteria, including a number of pathogens. MCPs consist of metabolic enzymes encapsulated within a protein shell. The main roles of MCPs are to concentrate enzymes together with their substrates (to increase reaction rates) and to sequester harmful metabolic intermediates. Prior studies indicate that MCPs have a selectively permeable protein shell, but the mechanisms that allow selective transport across the shell are not fully understood. Here we examine transport across the shell of the choline utilization (Cut) MCP of Escherichia coli 536, which has not been studied before. The shell of the Cut MCP is unusual in consisting of one pentameric and four hexameric bacterial microcompartment (BMC) domain proteins. It lacks trimeric shell proteins, which are thought to be required for the transport of larger substrates and enzymatic cofactors. In addition, its four hexameric BMC domain proteins are very similar in amino acid sequence. This raises questions about how the Cut MCP mediates the selective transport of the substrate, products and cofactors of choline metabolism. In this report, site-directed mutagenesis is used to modify the central pores (the main transport channels) of all four Cut BMC hexamers to assess their transport roles. Our findings indicate that a single shell protein, CmcB, plays the major role in choline transport across the shell of the Cut MCP and that the electrostatic properties of the CmcB pore also impact choline transport. The implications of these findings with regard to the higher-order structure of MCPs are discussed.
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Affiliation(s)
- Jessica M. Ochoa
- UCLA-Molecular Biology Institute, University of California, Los Angeles, USA
| | - Philip Dershwitz
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Mary Schappert
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Sharmistha Sinha
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Taylor I. Herring
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Todd O. Yeates
- UCLA-Molecular Biology Institute, University of California, Los Angeles, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 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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4
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Otoničar J, Hostnik M, Grundner M, Kostanjšek R, Gredar T, Garvas M, Arsov Z, Podlesek Z, Gostinčar C, Jakše J, Busby SJW, Butala M. A method for targeting a specified segment of DNA to a bacterial microorganelle. Nucleic Acids Res 2022; 50:e113. [PMID: 36029110 DOI: 10.1093/nar/gkac714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/28/2022] [Accepted: 08/09/2022] [Indexed: 11/14/2022] Open
Abstract
Encapsulation of a selected DNA molecule in a cell has important implications for bionanotechnology. Non-viral proteins that can be used as nucleic acid containers include proteinaceous subcellular bacterial microcompartments (MCPs) that self-assemble into a selectively permeable protein shell containing an enzymatic core. Here, we adapted a propanediol utilization (Pdu) MCP into a synthetic protein cage to package a specified DNA segment in vivo, thereby enabling subsequent affinity purification. To this end, we engineered the LacI transcription repressor to be routed, together with target DNA, into the lumen of a Strep-tagged Pdu shell. Sequencing of extracted DNA from the affinity-isolated MCPs shows that our strategy results in packaging of a DNA segment carrying multiple LacI binding sites, but not the flanking regions. Furthermore, we used LacI to drive the encapsulation of a DNA segment containing operators for LacI and for a second transcription factor.
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Affiliation(s)
- Jan Otoničar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maja Hostnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maja Grundner
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Rok Kostanjšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tajda Gredar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maja Garvas
- Jožef Stefan Institute, Condensed Matter Physics Department, 1000 Ljubljana, Slovenia
| | - Zoran Arsov
- Jožef Stefan Institute, Condensed Matter Physics Department, 1000 Ljubljana, Slovenia
| | - Zdravko Podlesek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Stephen J W Busby
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
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5
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Tasneem N, Szyszka TN, Jenner EN, Lau YH. How Pore Architecture Regulates the Function of Nanoscale Protein Compartments. ACS NANO 2022; 16:8540-8556. [PMID: 35583458 DOI: 10.1021/acsnano.2c02178] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Self-assembling proteins can form porous compartments that adopt well-defined architectures at the nanoscale. In nature, protein compartments act as semipermeable barriers to enable spatial separation and organization of complex biochemical processes. The compartment pores play a key role in their overall function by selectively controlling the influx and efflux of important biomolecular species. By engineering the pores, the functionality of compartments can be tuned to facilitate non-native applications, such as artificial nanoreactors for catalysis. In this review, we analyze how protein structure determines the porosity and impacts the function of both native and engineered compartments, highlighting the wealth of structural data recently obtained by cryo-EM and X-ray crystallography. Through this analysis, we offer perspectives on how current structural insights can inform future studies into the design of artificial protein compartments as nanoreactors with tunable porosity and function.
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Affiliation(s)
- Nuren Tasneem
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
| | - Taylor N Szyszka
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
- University of Sydney Nano Institute, Camperdown, New South Wales 2006, Australia
| | - Eric N Jenner
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
- University of Sydney Nano Institute, Camperdown, New South Wales 2006, Australia
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6
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Kumar G, Bari NK, Hazra JP, Sinha S. A major shell protein of 1,2-propanediol utilization microcompartment conserves the activity of its signature enzyme at higher temperatures. Chembiochem 2022; 23:e202100694. [PMID: 35229962 DOI: 10.1002/cbic.202100694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/28/2022] [Indexed: 11/11/2022]
Abstract
A classic example of an all-protein natural nano-bioreactor, the bacterial microcompartment is a special kind of prokaryotic organelle that confine enzymes within a small volume enveloped by an outer protein shell. These protein compartments metabolize specific organic molecules, allowing bacteria to survive in restricted nutrient environments. In this work, 1,2-propanediol utilization microcompartment (PduMCP) is used as a model to study the effect of molecular confinement on the stability and catalytic activity of native enzymes in microcompartment. A combination of enzyme assays, spectroscopic techniques, binding assays, and computational analysis are used to evaluate the impact of the major shell protein PduBB' on the stability and activity of PduMCP's signature enzyme, diol dehydratase PduCDE. While free PduCDE shows ~45% reduction in its optimum activity (activity at 37 o C) when exposed to a temperature of 45°C, it retains similar activity up to 50°C when encapsulated within PduMCP. PduBB', a major component of the outer shell of PduMCP, preserves the catalytic efficiency of PduCDE under thermal stress and prevents temperature-induced unfolding and aggregation of PduCDE in vitro . We observe that while both PduB and PduB' interact with the enzyme with micromolar affinity, only the PduBB' combination influences its activity and stability, highlighting the importance of the unique PduBB' combination in the functioning of PduMCP.
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Affiliation(s)
- Gaurav Kumar
- Institute of Nano Science and Technology, Chemical Biology Unit, Sector-81, Knowledge City, 140306, Mohali, INDIA
| | - Naimat Kalim Bari
- Institute of Nano Science and Technology, Chemical Biology Unit, Sector-81, Knowledge City, 140306, Mohali, INDIA
| | - Jagadish P Hazra
- Indian Institute of Science Education and Research Mohali, Chemical Sciences, Sector-81, Knowledge City, 140306, Mohali, INDIA
| | - Sharmistha Sinha
- Institute of Nano Science and Technology, Chemical Biology Unit, Sector-81, Knowledge City, 140306, Mohali, INDIA
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7
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Kaur S, Bari NK, Sinha S. Varying protein architectures in 3-dimensions for scaffolding and modulating properties of catalytic gold nanoparticles. Amino Acids 2022; 54:441-454. [PMID: 35103826 DOI: 10.1007/s00726-022-03127-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/13/2022] [Indexed: 11/01/2022]
Abstract
Fabrication and development of nanoscale materials with tunable structural and functional properties require a dynamic arrangement of nanoparticles on architectural templates. The function of nanoparticles not only depends on the property of the nanoparticles but also on their spatial orientations. Proteins with self-assembling properties which can be genetically engineered to varying architectural designs for scaffolds can be used to develop different orientations of nanoparticles in three dimensions. Here, we report the use of naturally self-assembling bacterial micro-compartment shell protein (PduA) assemblies in 2D and its single-point mutant variant (PduA[K26A]) in 3D architectures for the reduction and fabrication of gold nanoparticles. Interestingly, the different spatial organization of gold nanoparticles resulted in a smaller size in the 3D architect scaffold. Here, we observed a two-fold increase in catalytic activity and six-fold higher affinity toward TMB (3,3',5,5'-tetramethylbenzidine) substrate as a measure of higher peroxidase activity (nanozymatic) in the case of PduA[K26A] 3D scaffold. This approach demonstrates that the hierarchical organization of scaffold enables the fine-tuning of nanoparticle properties, thus paving the way toward the design of new nanoscale materials.
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Affiliation(s)
- Simerpreet Kaur
- Chemical Biology Unit, Institute of Nano Science and Technology (INST), Sector-81, Knowledge City, SAS Nagar Mohali, Punjab, 140306, India
| | - Naimat K Bari
- Chemical Biology Unit, Institute of Nano Science and Technology (INST), Sector-81, Knowledge City, SAS Nagar Mohali, Punjab, 140306, India
| | - Sharmistha Sinha
- Chemical Biology Unit, Institute of Nano Science and Technology (INST), Sector-81, Knowledge City, SAS Nagar Mohali, Punjab, 140306, India.
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8
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Goel D, Sinha S. Naturally occurring protein nano compartments: basic structure, function, and genetic engineering. NANO EXPRESS 2021. [DOI: 10.1088/2632-959x/ac2c93] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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9
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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: 21] [Impact Index Per Article: 5.3] [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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10
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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: 1.5] [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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11
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Recent structural insights into bacterial microcompartment shells. Curr Opin Microbiol 2021; 62:51-60. [PMID: 34058518 DOI: 10.1016/j.mib.2021.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/26/2021] [Accepted: 04/20/2021] [Indexed: 02/05/2023]
Abstract
Bacterial microcompartments are organelle-like structures that enhance a variety of metabolic functions in diverse bacteria. Composed entirely of proteins, thousands of homologous hexameric shell proteins tesselate to form facets while pentameric proteins form the vertices of a polyhedral shell that encapsulates various enzymes, substrates and cofactors. Recent structural data have highlighted nuanced variations in the sequence and topology of microcompartment shell proteins, emphasizing how variation and specialization enable the construction of complex molecular machines. Recent studies engineering synthetic miniaturized microcompartment shells provide additional frameworks for dissecting principles of microcompartment structure and assembly. This review updates our current understanding of bacterial microcompartment shell proteins, providing new insights and highlighting outstanding questions.
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12
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Li Y, Kennedy NW, Li S, Mills CE, Tullman-Ercek D, Olvera de la Cruz M. Computational and Experimental Approaches to Controlling Bacterial Microcompartment Assembly. ACS CENTRAL SCIENCE 2021; 7:658-670. [PMID: 34056096 PMCID: PMC8155464 DOI: 10.1021/acscentsci.0c01699] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 05/13/2023]
Abstract
Bacterial microcompartments compartmentalize the enzymes that aid chemical and energy production in many bacterial species. They are postulated to help bacteria survive in hostile environments. Metabolic engineers are interested in repurposing these organelles for non-native functions. Here, we use computational, theoretical, and experimental approaches to determine mechanisms that effectively control microcompartment self-assembly. We find, via multiscale modeling and mutagenesis studies, the interactions responsible for the binding of hexamer-forming proteins in a model system, the propanediol utilization bacterial microcompartments from Salmonella enterica serovar Typhimurium LT2. We determine how the changes in the microcompartment hexamer protein preferred angles and interaction strengths can modify the assembled morphologies. We demonstrate that such altered strengths and angles are achieved via amino acid mutations. A thermodynamic model provides guidelines to design microcompartments of various morphologies. These findings yield insight in controlled protein assembly and provide principles for assembling microcompartments for biochemical or energy applications as nanoreactors.
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Affiliation(s)
- Yaohua Li
- Department
of Material Science and Engineering, Northwestern
University, Evanston, Illinois 60208, United States
- Applied
Physics Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Nolan W. Kennedy
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary
Biological Sciences Graduate Program, Northwestern
University, Evanston, Illinois 60208, United States
| | - Siyu Li
- Department
of Material Science and Engineering, Northwestern
University, Evanston, Illinois 60208, United States
| | - Carolyn E. Mills
- 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
- E-mail:
| | - Monica Olvera de la Cruz
- Department
of Material Science and Engineering, Northwestern
University, Evanston, Illinois 60208, United States
- Applied
Physics Program, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- E-mail:
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13
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Kaur H, Bari NK, Garg A, Sinha S. Protein morphology drives the structure and catalytic activity of bio-inorganic hybrids. Int J Biol Macromol 2021; 176:106-116. [PMID: 33556398 DOI: 10.1016/j.ijbiomac.2021.01.217] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 11/26/2022]
Abstract
Bio-hybrid materials have received a lot of attention in view of their bio-mimicking nature. One such biomimetic material with catalytic activity are the protein derived floral nanohybrid. Copper phosphate coordinated flakes can be curated to distinct floral morphology using proteins. Structurally two different proteins with similar size and with no known enzymatic activity are used to evaluate the role of protein structure and morphology, on the structure-activity relationship of the developed hybrid nanoflowers. Globular protein BSA and bacterial microcompartment domain protein PduBB' are selected. PduBB' because of self-assembling nature forms extended sheets, whereas BSA lacks specific assembly. The developed hybrid NFs differ in their morphology and also in their mimicry as a biological catalyst. The present investigation highlights the importance of the quaternary structure of proteins in tailoring the structure and function of the h-NFs. The results in this manuscript will motivate and guide designing, engineering and selection of glue material for fabricating biomacromolecule derived biohybrid material to mimic natural enzymes of potential industrial application.
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Affiliation(s)
- Harpreet Kaur
- Chemical Biology Unit, Institute of Nano Science and Technology (INST), Sector-81, Knowledge City, SAS Nagar Mohali, Punjab 140306, India
| | - Naimat K Bari
- Chemical Biology Unit, Institute of Nano Science and Technology (INST), Sector-81, Knowledge City, SAS Nagar Mohali, Punjab 140306, India
| | - Ankush Garg
- Chemical Biology Unit, Institute of Nano Science and Technology (INST), Sector-81, Knowledge City, SAS Nagar Mohali, Punjab 140306, India
| | - Sharmistha Sinha
- Chemical Biology Unit, Institute of Nano Science and Technology (INST), Sector-81, Knowledge City, SAS Nagar Mohali, Punjab 140306, India.
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14
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Kennedy NW, Ikonomova SP, Slininger Lee M, Raeder HW, Tullman-Ercek D. Self-assembling Shell Proteins PduA and PduJ have Essential and Redundant Roles in Bacterial Microcompartment Assembly. J Mol Biol 2020; 433:166721. [PMID: 33227310 DOI: 10.1016/j.jmb.2020.11.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 01/21/2023]
Abstract
Protein self-assembly is a common and essential biological phenomenon, and bacterial microcompartments present a promising model system to study this process. Bacterial microcompartments are large, protein-based organelles which natively carry out processes important for carbon fixation in cyanobacteria and the survival of enteric bacteria. These structures are increasingly popular with biological engineers due to their potential utility as nanobioreactors or drug delivery vehicles. However, the limited understanding of the assembly mechanism of these bacterial microcompartments hinders efforts to repurpose them for non-native functions. Here, we comprehensively investigate proteins involved in the assembly of the 1,2-propanediol utilization bacterial microcompartment from Salmonella enterica serovar Typhimurium LT2, one of the most widely studied microcompartment systems. We first demonstrate that two shell proteins, PduA and PduJ, have a high propensity for self-assembly upon overexpression, and we provide a novel method for self-assembly quantification. Using genomic knock-outs and knock-ins, we systematically show that these two proteins play an essential and redundant role in bacterial microcompartment assembly that cannot be compensated by other shell proteins. At least one of the two proteins PduA and PduJ must be present for the bacterial microcompartment shell to assemble. We also demonstrate that assembly-deficient variants of these proteins are unable to rescue microcompartment formation, highlighting the importance of this assembly property. Our work provides insight into the assembly mechanism of these bacterial organelles and will aid downstream engineering efforts.
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Affiliation(s)
- Nolan W Kennedy
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, United States
| | - Svetlana P Ikonomova
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - Marilyn Slininger Lee
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States; US Army Combat Capabilities Development Command Chemical Biological Center, Edgewood, MD, United States
| | - Henry W Raeder
- Molecular Biosciences Program, Weinberg College of Arts and Sciences, Northwestern University, Evanston, IL, United States
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States; Center for Synthetic Biology, Northwestern University, Evanston, IL, United States.
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15
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Probe into a multi-protein prokaryotic organelle using thermal scanning assay reveals distinct properties of the core and the shell. Biochim Biophys Acta Gen Subj 2020; 1864:129680. [DOI: 10.1016/j.bbagen.2020.129680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022]
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16
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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: 21] [Impact Index Per Article: 4.2] [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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17
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Ochoa JM, Nguyen VN, Nie M, Sawaya MR, Bobik TA, Yeates TO. Symmetry breaking and structural polymorphism in a bacterial microcompartment shell protein for choline utilization. Protein Sci 2020; 29:2201-2212. [PMID: 32885887 DOI: 10.1002/pro.3941] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 01/02/2023]
Abstract
Bacterial microcompartments are protein-based organelles that carry out specialized metabolic functions in diverse bacteria. Their outer shells are built from several thousand protein subunits. Some of the architectural principles of bacterial microcompartments have been articulated, with lateral packing of flat hexameric BMC proteins providing the basic foundation for assembly. Nonetheless, a complete understanding has been elusive, partly owing to polymorphic mechanisms of assembly exhibited by most microcompartment types. An earlier study of one homologous BMC shell protein subfamily, EutS/PduU, revealed a profoundly bent, rather than flat, hexameric structure. The possibility of a specialized architectural role was hypothesized, but artifactual effects of crystallization could not be ruled out. Here we report a series of crystal structures of an orthologous protein, CutR, from a glycyl-radical type choline-utilizing microcompartment from the bacterium Streptococcus intermedius. Depending on crystal form, expression construct, and minor mutations, a range of novel quaternary architectures was observed, including two spiral hexagonal assemblies. A new graphical approach helps illuminate the variations in BMC hexameric structure, with results substantiating the idea that the EutS/PduU/CutR subfamily of BMC proteins may endow microcompartment shells with flexible modes of assembly.
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Affiliation(s)
- Jessica M Ochoa
- UCLA-Molecular Biology Institute, University of California, Los Angeles (UCLA), California, Los Angeles, USA
| | - Vy N Nguyen
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), California, Los Angeles, USA
| | - Mengxiao Nie
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), California, Los Angeles, USA
| | - Michael R Sawaya
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles (UCLA), California, Los Angeles, USA
| | - Thomas A Bobik
- Department of Biochemistry, Biophysics and Molecular Biology; Iowa State University, Ames, Iowa, USA
| | - Todd O Yeates
- UCLA-Molecular Biology Institute, University of California, Los Angeles (UCLA), California, Los Angeles, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), California, Los Angeles, USA.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles (UCLA), California, Los Angeles, USA
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18
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Decoding the stoichiometric composition and organisation of bacterial metabolosomes. Nat Commun 2020; 11:1976. [PMID: 32332738 PMCID: PMC7181861 DOI: 10.1038/s41467-020-15888-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 03/31/2020] [Indexed: 01/08/2023] Open
Abstract
Some enteric bacteria including Salmonella have evolved the propanediol-utilising microcompartment (Pdu MCP), a specialised proteinaceous organelle that is essential for 1,2-propanediol degradation and enteric pathogenesis. Pdu MCPs are a family of bacterial microcompartments that are self-assembled from hundreds of proteins within the bacterial cytosol. Here, we seek a comprehensive understanding of the stoichiometric composition and organisation of Pdu MCPs. We obtain accurate stoichiometry of shell proteins and internal enzymes of the natural Pdu MCP by QconCAT-driven quantitative mass spectrometry. Genetic deletion of the major shell protein and absolute quantification reveal the stoichiometric and structural remodelling of metabolically functional Pdu MCPs. Decoding the precise protein stoichiometry allows us to develop an organisational model of the Pdu metabolosome. The structural insights into the Pdu MCP are critical for both delineating the general principles underlying bacterial organelle formation, structural robustness and function, and repurposing natural microcompartments using synthetic biology for biotechnological applications. Enteric pathogens such as Salmonella depend on propanediol-utilising microcompartments (Pdu MCP), which self-assemble from cytosolic proteins. Using mass spectrometry-based absolute quantification, the authors here define the protein stoichiometry and propose an organizational model of a Salmonella Pdu MCP.
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19
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Genetic Characterization of a Glycyl Radical Microcompartment Used for 1,2-Propanediol Fermentation by Uropathogenic Escherichia coli CFT073. J Bacteriol 2020; 202:JB.00017-20. [PMID: 32071097 DOI: 10.1128/jb.00017-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/13/2020] [Indexed: 12/29/2022] Open
Abstract
Bacterial microcompartments (MCPs) are widespread protein-based organelles composed of metabolic enzymes encapsulated within a protein shell. The function of MCPs is to optimize metabolic pathways by confining toxic and/or volatile pathway intermediates. A major class of MCPs known as glycyl radical MCPs has only been partially characterized. Here, we show that uropathogenic Escherichia coli CFT073 uses a glycyl radical MCP for 1,2-propanediol (1,2-PD) fermentation. Bioinformatic analyses identified a large gene cluster (named grp for glycyl radical propanediol) that encodes homologs of a glycyl radical diol dehydratase, other 1,2-PD catabolic enzymes, and MCP shell proteins. Growth studies showed that E. coli CFT073 grows on 1,2-PD under anaerobic conditions but not under aerobic conditions. All 19 grp genes were individually deleted, and 8/19 were required for 1,2-PD fermentation. Electron microscopy and genetic studies showed that a bacterial MCP is involved. Bioinformatics combined with genetic analyses support a proposed pathway of 1,2-PD degradation and suggest that enzymatic cofactors are recycled internally within the Grp MCP. A two-component system (grpP and grpQ) is shown to mediate induction of the grp locus by 1,2-PD. Tests of the E. coli Reference (ECOR) collection indicate that >10% of E. coli strains ferment 1,2-PD using a glycyl radical MCP. In contrast to other MCP systems, individual deletions of MCP shell genes (grpE, grpH, and grpI) eliminated 1,2-PD catabolism, suggesting significant functional differences with known MCPs. Overall, the studies presented here are the first comprehensive genetic analysis of a Grp-type MCP.IMPORTANCE Bacterial MCPs have a number of potential biotechnology applications and have been linked to bacterial pathogenesis, cancer, and heart disease. Glycyl radical MCPs are a large but understudied class of bacterial MCPs. Here, we show that uropathogenic E. coli CFT073 uses a glycyl radical MCP for 1,2-PD fermentation, and we conduct a comprehensive genetic analysis of the genes involved. Studies suggest significant functional differences between the glycyl radical MCP of E. coli CFT073 and better-studied MCPs. They also provide a foundation for building a deeper general understanding of glycyl radical MCPs in an organism where sophisticated genetic methods are available.
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20
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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: 2.0] [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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21
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Kalnins G, Cesle EE, Jansons J, Liepins J, Filimonenko A, Tars K. Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles. Nat Commun 2020; 11:388. [PMID: 31959751 PMCID: PMC6971018 DOI: 10.1038/s41467-019-14205-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/18/2019] [Indexed: 11/08/2022] Open
Abstract
Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We conclude that the enzymatic core is encapsulated in a hierarchical manner and that the CutC choline lyase may play a secondary role as an adaptor protein. We also present a cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle at 3.3 Å resolution, and demonstrate variability among the minor shell forms.
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Affiliation(s)
- Gints Kalnins
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia.
| | - Eva-Emilija Cesle
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
| | - Juris Jansons
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, Riga, 1004, Latvia
| | - Anatolij Filimonenko
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
- University of Latvia, Jelgavas 1, Riga, 1004, Latvia
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22
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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: 2.4] [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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23
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Bari NK, Kumar G, Hazra JP, Kaur S, Sinha S. Functional protein shells fabricated from the self-assembling protein sheets of prokaryotic organelles. J Mater Chem B 2020; 8:523-533. [DOI: 10.1039/c9tb02224d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fabricating single component protein compartments from the shells proteins of bacterial microcompartments.
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Affiliation(s)
- Naimat K. Bari
- Institute of Nano Science and Technology
- Habitat Centre
- Sector-64
- Mohali
- India
| | - Gaurav Kumar
- Institute of Nano Science and Technology
- Habitat Centre
- Sector-64
- Mohali
- India
| | - Jagadish P. Hazra
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER)
- Mohali
- Knowledge City
- Sector 81
| | - Simerpreet Kaur
- Institute of Nano Science and Technology
- Habitat Centre
- Sector-64
- Mohali
- India
| | - Sharmistha Sinha
- Institute of Nano Science and Technology
- Habitat Centre
- Sector-64
- Mohali
- India
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24
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Garcia-Alles LF, Root K, Maveyraud L, Aubry N, Lesniewska E, Mourey L, Zenobi R, Truan G. Occurrence and stability of hetero-hexamer associations formed by β-carboxysome CcmK shell components. PLoS One 2019; 14:e0223877. [PMID: 31603944 PMCID: PMC6788708 DOI: 10.1371/journal.pone.0223877] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022] Open
Abstract
The carboxysome is a bacterial micro-compartment (BMC) subtype that encapsulates enzymatic activities necessary for carbon fixation. Carboxysome shells are composed of a relatively complex cocktail of proteins, their precise number and identity being species dependent. Shell components can be classified in two structural families, the most abundant class associating as hexamers (BMC-H) that are supposed to be major players for regulating shell permeability. Up to recently, these proteins were proposed to associate as homo-oligomers. Genomic data, however, demonstrated the existence of paralogs coding for multiple shell subunits. Here, we studied cross-association compatibilities among BMC-H CcmK proteins of Synechocystis sp. PCC6803. Co-expression in Escherichia coli proved a consistent formation of hetero-hexamers combining CcmK1 and CcmK2 or, remarkably, CcmK3 and CcmK4 subunits. Unlike CcmK1/K2 hetero-hexamers, the stoichiometry of incorporation of CcmK3 in associations with CcmK4 was low. Cross-interactions implicating other combinations were weak, highlighting a structural segregation of the two groups that could relate to gene organization. Sequence analysis and structural models permitted the localization of interactions that would favor formation of CcmK3/K4 hetero-hexamers. The crystallization of these CcmK3/K4 associations conducted to the elucidation of a structure corresponding to the CcmK4 homo-hexamer. Yet, subunit exchange could not be demonstrated in vitro. Biophysical measurements showed that hetero-hexamers are thermally less stable than homo-hexamers, and impeded in forming larger assemblies. These novel findings are discussed within the context of reported data to propose a functional scenario in which minor CcmK3/K4 incorporation in shells would introduce sufficient local disorder as to allow shell remodeling necessary to adapt rapidly to environmental changes.
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Affiliation(s)
- Luis F. Garcia-Alles
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- * E-mail:
| | - Katharina Root
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Laurent Maveyraud
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nathalie Aubry
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Eric Lesniewska
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Lionel Mourey
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Gilles Truan
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
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25
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Sommer M, Sutter M, Gupta S, Kirst H, Turmo A, Lechno-Yossef S, Burton RL, Saechao C, Sloan NB, Cheng X, Chan LJG, Petzold CJ, Fuentes-Cabrera M, Ralston CY, Kerfeld CA. Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells. PLANT PHYSIOLOGY 2019; 179:156-167. [PMID: 30389783 PMCID: PMC6324227 DOI: 10.1104/pp.18.01190] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/26/2018] [Indexed: 05/10/2023]
Abstract
Bacterial microcompartments (BMCs) encapsulate enzymes within a selectively permeable, proteinaceous shell. Carboxysomes are BMCs containing ribulose-1,5-bisphosphate carboxylase oxygenase and carbonic anhydrase that enhance carbon dioxide fixation. The carboxysome shell consists of three structurally characterized protein types, each named after the oligomer they form: BMC-H (hexamer), BMC-P (pentamer), and BMC-T (trimer). These three protein types form cyclic homooligomers with pores at the center of symmetry that enable metabolite transport across the shell. Carboxysome shells contain multiple BMC-H paralogs, each with distinctly conserved residues surrounding the pore, which are assumed to be associated with specific metabolites. We studied the regulation of β-carboxysome shell composition by investigating the BMC-H genes ccmK3 and ccmK4 situated in a locus remote from other carboxysome genes. We made single and double deletion mutants of ccmK3 and ccmK4 in Synechococcus elongatus PCC7942 and show that, unlike CcmK3, CcmK4 is necessary for optimal growth. In contrast to other CcmK proteins, CcmK3 does not form homohexamers; instead CcmK3 forms heterohexamers with CcmK4 with a 1:2 stoichiometry. The CcmK3-CcmK4 heterohexamers form stacked dodecamers in a pH-dependent manner. Our results indicate that CcmK3-CcmK4 heterohexamers potentially expand the range of permeability properties of metabolite channels in carboxysome shells. Moreover, the observed facultative formation of dodecamers in solution suggests that carboxysome shell permeability may be dynamically attenuated by "capping" facet-embedded hexamers with a second hexamer. Because β-carboxysomes are obligately expressed, heterohexamer formation and capping could provide a rapid and reversible means to alter metabolite flux across the shell in response to environmental/growth conditions.
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Affiliation(s)
- Manuel Sommer
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Markus Sutter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Sayan Gupta
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Henning Kirst
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Aiko Turmo
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Sigal Lechno-Yossef
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Rodney L Burton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Christine Saechao
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Nancy B Sloan
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy and Biophysics Graduate Program, Ohio State University, Columbus, Ohio 43210
| | - Leanne-Jade G Chan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Miguel Fuentes-Cabrera
- Center for Nanophase Materials Sciences and Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennesse 37831
| | - Corie Y Ralston
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Cheryl A Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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Bari NK, Kumar G, Bhatt A, Hazra JP, Garg A, Ali ME, Sinha S. Nanoparticle Fabrication on Bacterial Microcompartment Surface for the Development of Hybrid Enzyme-Inorganic Catalyst. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02322] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Naimat Kalim Bari
- Institute of Nano Science and Technology (INST), Phase-10, Sector-64, Mohali, Punjab 160062, India
| | - Gaurav Kumar
- Institute of Nano Science and Technology (INST), Phase-10, Sector-64, Mohali, Punjab 160062, India
| | - Aashish Bhatt
- Institute of Nano Science and Technology (INST), Phase-10, Sector-64, Mohali, Punjab 160062, India
| | - Jagadish Prasad Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, Mohali, Punjab 140306, India
| | - Ankush Garg
- Institute of Nano Science and Technology (INST), Phase-10, Sector-64, Mohali, Punjab 160062, India
| | - Md. Ehesan Ali
- Institute of Nano Science and Technology (INST), Phase-10, Sector-64, Mohali, Punjab 160062, India
| | - Sharmistha Sinha
- Institute of Nano Science and Technology (INST), Phase-10, Sector-64, Mohali, Punjab 160062, India
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27
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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: 3.9] [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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28
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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: 4.9] [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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29
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The Wrappers of the 1,2-Propanediol Utilization Bacterial Microcompartments. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1112:333-344. [DOI: 10.1007/978-981-13-3065-0_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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30
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Slininger Lee MF, Jakobson CM, Tullman-Ercek D. Evidence for Improved Encapsulated Pathway Behavior in a Bacterial Microcompartment through Shell Protein Engineering. ACS Synth Biol 2017; 6:1880-1891. [PMID: 28585808 DOI: 10.1021/acssynbio.7b00042] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial microcompartments are a class of proteinaceous organelles comprising a characteristic protein shell enclosing a set of enzymes. Compartmentalization can prevent escape of volatile or toxic intermediates, prevent off-pathway reactions, and create private cofactor pools. Encapsulation in synthetic microcompartment organelles will enhance the function of heterologous pathways, but to do so, it is critical to understand how to control diffusion in and out of the microcompartment organelle. To this end, we explored how small differences in the shell protein structure result in changes in the diffusion of metabolites through the shell. We found that the ethanolamine utilization (Eut) protein EutM properly incorporates into the 1,2-propanediol utilization (Pdu) microcompartment, altering native metabolite accumulation and the resulting growth on 1,2-propanediol as the sole carbon source. Further, we identified a single pore-lining residue mutation that confers the same phenotype as substitution of the full EutM protein, indicating that small molecule diffusion through the shell is the cause of growth enhancement. Finally, we show that the hydropathy index and charge of pore amino acids are important indicators to predict how pore mutations will affect growth on 1,2-propanediol, likely by controlling diffusion of one or more metabolites. This study highlights the use of two strategies to engineer microcompartments to control metabolite transport: altering the existing shell protein pore via mutation of the pore-lining residues, and generating chimeras using shell proteins with the desired pores.
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Affiliation(s)
- Marilyn F. Slininger Lee
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Christopher M. Jakobson
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department
of Chemical and Systems Biology, Stanford University, Stanford, California, 94305, United States
| | - Danielle Tullman-Ercek
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208-3120, United States
- Chemistry
of Life Processes Institute, Northwestern University, 2170 Campus
Drive, Evanston, Illinois 60208-3120, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological Institute B486, Evanston, Illinois 60208-3120, United States
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31
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Graf L, Wu K, Wilson JW. Transfer and analysis of Salmonella pdu genes in a range of Gram-negative bacteria demonstrate exogenous microcompartment expression across a variety of species. Microb Biotechnol 2017; 11:199-210. [PMID: 28967207 PMCID: PMC5743805 DOI: 10.1111/1751-7915.12863] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/17/2017] [Accepted: 08/31/2017] [Indexed: 12/21/2022] Open
Abstract
Bacterial microcompartments (MCPs) are protein organelles that typically house toxic or volatile reaction intermediates involved in metabolic pathways. Engineering bacteria to express exogenous MCPs will allow these cells to gain useful functions involving molecule compartmentalization. We cloned a 38 kb region from the Salmonella enterica serovar Typhimurium genome containing the pdu 1,2 propanediol (1,2 PD) utilization and cob/cbi genes using the FRT‐Capture strategy to clone and transfer large genomic segments. We transferred this clone to a range of Gram‐negative bacteria and found the clone to be functional for 1,2 PD metabolism in a variety of species including S. Typhimurium Δpdu, Escherichia coli, Salmonella bongori, Klebsiella pneumoniae, Cronobacter sakazakii, Serratia marcescens, and different Pseudomonas species. We successfully isolated MCPs expressed from the clone from several, but not all, of these strains, and we observed this utilizing a range of different media and in the absence of protease inhibitor. We also present a mini‐prep protocol that allows rapid, small‐scale screening of strains for MCP production. To date, this is the first analysis of cloned, exogenous microcompartment expression across several different Gram‐negative backgrounds and provides a foundation for MCP use in a variety of bacterial species using a full, intact clone.
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Affiliation(s)
- Laura Graf
- Biology Department, Villanova University, Mendel Hall, 800 Lancaster Avenue, Villanova, PA, 19085, USA
| | - Kent Wu
- Biology Department, Villanova University, Mendel Hall, 800 Lancaster Avenue, Villanova, PA, 19085, USA
| | - James W Wilson
- Biology Department, Villanova University, Mendel Hall, 800 Lancaster Avenue, Villanova, PA, 19085, USA
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32
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Chen L, Hatti-Kaul R. Exploring Lactobacillus reuteri DSM20016 as a biocatalyst for transformation of longer chain 1,2-diols: Limits with microcompartment. PLoS One 2017; 12:e0185734. [PMID: 28957423 PMCID: PMC5619818 DOI: 10.1371/journal.pone.0185734] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/18/2017] [Indexed: 11/18/2022] Open
Abstract
Lactobacillus reuteri metabolises glycerol efficiently to form 3-hydroxypropionic acid (3-HP) and 1,3-propanediol (1,3PDO) by the same mechanism as that for 1,2-propanediol (1,2PDO) conversion to propionic acid and propanol via its propanediol utilization (pdu) pathway. Pdu enzymes are encoded by the pdu-operon, which also contain genes encoding the shell proteins of the microcompartment housing the metabolic pathway. In this work the selectivity and kinetics of the reactions catalysed by L. reuteri DSM20016 Pdu enzymes glycerol dehydratase (GDH), 1,3-propanediol oxidoreductase (PduQ) and coenzyme-A acylating propionaldehyde dehydrogenase (PduP), produced recombinantly, was investigated against corresponding substrates of different chain lengths. Glycerol dehydratase exhibited activity against C2-C4 polyols, with the highest activity against glycerol and 1,2-propanediol (1,2-PDO). A double mutant of the pduC gene of GDH (PduC-S302A/Q337A) was constructed that displayed lowered activity against glycerol and 1,2PDO but extended the substrate range upto C6-diol. The best substrate for both PduQ and PduP was 3-hydroxypropanal (3HPA), although PduP exhibited nearly 10-fold higher specific activity. The enzymes also showed some activity against C3-C10 aliphatic aldehydes, with PduP having higher relative activity. Subsequently, transformation of polyols using whole cells of L. reuteri containing the wild type- and mutated GDH, respectively, confirmed the reduced activity of the mutant against glycerol and 1,2PDO, but its activity against longer substrates was negligible. In contrast, recombinant Escherichia coli BL21(DE3) cells harboring the GDH variant converted diols with up to C6 carbon chain length to their respective aldehydes, suggesting that the protein shell of the microcompartment in L. reuteri posed a barrier to the passage of longer chain substrate.
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Affiliation(s)
- Lu Chen
- Division of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
- * E-mail:
| | - Rajni Hatti-Kaul
- Division of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
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33
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Garcia-Alles LF, Lesniewska E, Root K, Aubry N, Pocholle N, Mendoza CI, Bourillot E, Barylyuk K, Pompon D, Zenobi R, Reguera D, Truan G. Spontaneous non-canonical assembly of CcmK hexameric components from β-carboxysome shells of cyanobacteria. PLoS One 2017; 12:e0185109. [PMID: 28934279 PMCID: PMC5608322 DOI: 10.1371/journal.pone.0185109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/06/2017] [Indexed: 02/07/2023] Open
Abstract
CcmK proteins are major constituents of icosahedral shells of β-carboxysomes, a bacterial microcompartment that plays a key role for CO2 fixation in nature. Supported by the characterization of bidimensional (2D) layers of packed CcmK hexamers in crystal and electron microscopy structures, CcmK are assumed to be the major components of icosahedral flat facets. Here, we reassessed the validity of this model by studying CcmK isoforms from Synechocystis sp. PCC6803. Native mass spectrometry studies confirmed that CcmK are hexamers in solution. Interestingly, potential pre-assembled intermediates were also detected with CcmK2. Atomic-force microscopy (AFM) imaging under quasi-physiological conditions confirmed the formation of canonical flat sheets with CcmK4. Conversely, CcmK2 formed both canonical and striped-patterned patches, while CcmK1 assembled into remarkable supra-hexameric curved honeycomb-like mosaics. Mutational studies ascribed the propensity of CcmK1 to form round assemblies to a combination of two features shared by at least one CcmK isoform in most β-cyanobacteria: a displacement of an α helical portion towards the hexamer edge, where a potential phosphate binding funnel forms between packed hexamers, and the presence of a short C-terminal extension in CcmK1. All-atom molecular dynamics supported a contribution of phosphate molecules sandwiched between hexamers to bend CcmK1 assemblies. Formation of supra-hexameric curved structures could be reproduced in coarse-grained simulations, provided that adhesion forces to the support were weak. Apart from uncovering unprecedented CcmK self-assembly features, our data suggest the possibility that transitions between curved and flat assemblies, following cargo maturation, could be important for the biogenesis of β-carboxysomes, possibly also of other BMC.
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Affiliation(s)
- Luis F. Garcia-Alles
- LISBP, CNRS, INRA, INSA, University of Toulouse, Toulouse, France
- * E-mail: (LFGA); (GT)
| | - Eric Lesniewska
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Katharina Root
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Nathalie Aubry
- LISBP, CNRS, INRA, INSA, University of Toulouse, Toulouse, France
| | - Nicolas Pocholle
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Carlos I. Mendoza
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Cd Mx, México
| | - Eric Bourillot
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Denis Pompon
- LISBP, CNRS, INRA, INSA, University of Toulouse, Toulouse, France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - David Reguera
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
| | - Gilles Truan
- LISBP, CNRS, INRA, INSA, University of Toulouse, Toulouse, France
- * E-mail: (LFGA); (GT)
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34
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Young EJ, Burton R, Mahalik JP, Sumpter BG, Fuentes-Cabrera M, Kerfeld CA, Ducat DC. Engineering the Bacterial Microcompartment Domain for Molecular Scaffolding Applications. Front Microbiol 2017; 8:1441. [PMID: 28824573 PMCID: PMC5534457 DOI: 10.3389/fmicb.2017.01441] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/17/2017] [Indexed: 01/03/2023] Open
Abstract
As synthetic biology advances the intricacy of engineered biological systems, the importance of spatial organization within the cellular environment must not be marginalized. Increasingly, biological engineers are investigating means to control spatial organization within the cell, mimicking strategies used by natural pathways to increase flux and reduce cross-talk. A modular platform for constructing a diverse set of defined, programmable architectures would greatly assist in improving yields from introduced metabolic pathways and increasing insulation of other heterologous systems. Here, we review recent research on the shell proteins of bacterial microcompartments and discuss their potential application as "building blocks" for a range of customized intracellular scaffolds. We summarize the state of knowledge on the self-assembly of BMC shell proteins and discuss future avenues of research that will be important to realize the potential of BMC shell proteins as predictively assembling and programmable biological materials for bioengineering.
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Affiliation(s)
- Eric J. Young
- Biochemistry and Molecular Biology, Michigan State University, East LansingMI, United States
- MSU-DOE Plant Research Laboratory, East LansingMI, United States
| | - Rodney Burton
- MSU-DOE Plant Research Laboratory, East LansingMI, United States
| | - Jyoti P. Mahalik
- Computational Sciences and Engineering, Oak Ridge National Laboratory, Oak RidgeTN, United States
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak RidgeTN, United States
| | - Bobby G. Sumpter
- Computational Sciences and Engineering, Oak Ridge National Laboratory, Oak RidgeTN, United States
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak RidgeTN, United States
| | - Miguel Fuentes-Cabrera
- Computational Sciences and Engineering, Oak Ridge National Laboratory, Oak RidgeTN, United States
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak RidgeTN, United States
| | - Cheryl A. Kerfeld
- Biochemistry and Molecular Biology, Michigan State University, East LansingMI, United States
- MSU-DOE Plant Research Laboratory, East LansingMI, United States
- Molecular Biophysics and Integrated Bioimaging Division, Berkeley National Laboratory, BerkeleyCA, United States
| | - Daniel C. Ducat
- Biochemistry and Molecular Biology, Michigan State University, East LansingMI, United States
- MSU-DOE Plant Research Laboratory, East LansingMI, United States
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35
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Sommer M, Cai F, Melnicki M, Kerfeld CA. β-Carboxysome bioinformatics: identification and evolution of new bacterial microcompartment protein gene classes and core locus constraints. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3841-3855. [PMID: 28419380 PMCID: PMC5853843 DOI: 10.1093/jxb/erx115] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/18/2017] [Indexed: 05/03/2023]
Abstract
Carboxysomes are bacterial microcompartments (BMCs) that enhance CO2 fixation in all cyanobacteria. Structurally, carboxysome shell proteins are classified according to the type of oligomer formed: hexameric (BMC-H), trimeric (BMC-T) and pentameric (BMC-P) proteins. To understand the forces driving the evolution of the carboxysome shell, we conducted a bioinformatic study of genes encoding β-carboxysome shell proteins, taking advantage of the recent large increase in sequenced cyanobacterial genomes. In addition to the four well-established BMC-H (CcmK1-4) classes, our analysis reveals two new CcmK classes, which we name CcmK5 and CcmK6. CcmK5 is phylogenetically closest to CcmK3 and CcmK4, and the ccmK5 gene is found only in genomes lacking ccmK3 and ccmk4 genes. ccmK6 is found predominantly in heterocyst-forming cyanobacteria. The gene encoding the BMC-T homolog CcmO is associated with the main carboxysome locus (MCL) in only 60% of all species. We find five evolutionary origins of separation of ccmO from the MCL. Transcriptome analysis demonstrates that satellite ccmO genes, in contrast to MCL-associated ccmO genes, are never co-regulated with other MCL genes. The dispersal of carboxysome shell genes across the genome allows for distinct regulation of their expression, perhaps in response to changes in environmental conditions.
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Affiliation(s)
- Manuel Sommer
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fei Cai
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew Melnicki
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cheryl A Kerfeld
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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36
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The N Terminus of the PduB Protein Binds the Protein Shell of the Pdu Microcompartment to Its Enzymatic Core. J Bacteriol 2017; 199:JB.00785-16. [PMID: 28138097 DOI: 10.1128/jb.00785-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/20/2017] [Indexed: 12/12/2022] Open
Abstract
Bacterial microcompartments (MCPs) are extremely large proteinaceous organelles that consist of an enzymatic core encapsulated within a complex protein shell. A key question in MCP biology is the nature of the interactions that guide the assembly of thousands of protein subunits into a well-ordered metabolic compartment. In this report, we show that the N-terminal 37 amino acids of the PduB protein have a critical role in binding the shell of the 1,2-propanediol utilization (Pdu) microcompartment to its enzymatic core. Several mutations were constructed that deleted short regions of the N terminus of PduB. Growth tests indicated that three of these deletions were impaired MCP assembly. Attempts to purify MCPs from these mutants, followed by gel electrophoresis and enzyme assays, indicated that the protein complexes isolated consisted of MCP shells depleted of core enzymes. Electron microscopy substantiated these findings by identifying apparently empty MCP shells but not intact MCPs. Analyses of 13 site-directed mutants indicated that the key region of the N terminus of PduB required for MCP assembly is a putative helix spanning residues 6 to 18. Considering the findings presented here together with prior work, we propose a new model for MCP assembly.IMPORTANCE Bacterial microcompartments consist of metabolic enzymes encapsulated within a protein shell and are widely used to optimize metabolic process. Here, we show that the N-terminal 37 amino acids of the PduB shell protein are essential for assembly of the 1,2-propanediol utilization microcompartment. The results indicate that it plays a key role in binding the outer shell to the enzymatic core. We propose that this interaction might be used to define the relative orientation of the shell with respect to the core. This finding is of fundamental importance to our understanding of microcompartment assembly and may have application to engineering microcompartments as nanobioreactors for chemical production.
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37
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Gan Q, Lehman BP, Bobik TA, Fan C. Expanding the genetic code of Salmonella with non-canonical amino acids. Sci Rep 2016; 6:39920. [PMID: 28008993 PMCID: PMC5180212 DOI: 10.1038/srep39920] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/29/2016] [Indexed: 12/21/2022] Open
Abstract
The diversity of non-canonical amino acids (ncAAs) endows proteins with new features for a variety of biological studies and biotechnological applications. The genetic code expansion strategy, which co-translationally incorporates ncAAs into specific sites of target proteins, has been applied in many organisms. However, there have been only few studies on pathogens using genetic code expansion. Here, we introduce this technique into the human pathogen Salmonella by incorporating p-azido-phenylalanine, benzoyl-phenylalanine, acetyl-lysine, and phosphoserine into selected Salmonella proteins including a microcompartment shell protein (PduA), a type III secretion effector protein (SteA), and a metabolic enzyme (malate dehydrogenase), and demonstrate practical applications of genetic code expansion in protein labeling, photocrosslinking, and post-translational modification studies in Salmonella. This work will provide powerful tools for a wide range of studies on Salmonella.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Brent P Lehman
- 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
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
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38
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Mallette E, Kimber MS. A Complete Structural Inventory of the Mycobacterial Microcompartment Shell Proteins Constrains Models of Global Architecture and Transport. J Biol Chem 2016; 292:1197-1210. [PMID: 27927988 DOI: 10.1074/jbc.m116.754093] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/05/2016] [Indexed: 11/06/2022] Open
Abstract
Bacterial microcompartments are bacterial analogs of eukaryotic organelles in that they spatially segregate aspects of cellular metabolism, but they do so by building not a lipid membrane but a thin polyhedral protein shell. Although multiple shell protein structures are known for several microcompartment types, additional uncharacterized components complicate systematic investigations of shell architecture. We report here the structures of all four proteins proposed to form the shell of an uncharacterized microcompartment designated the Rhodococcus and Mycobacterium microcompartment (RMM), which, along with crystal interactions and docking studies, suggests possible models for the particle's vertex and edge organization. MSM0272 is a typical hexameric β-sandwich shell protein thought to form the bulk of the facet. MSM0273 is a pentameric β-barrel shell protein that likely plugs the vertex of the particle. MSM0271 is an unusual double-ringed bacterial microcompartment shell protein whose rings are organized in an offset position relative to all known related proteins. MSM0275 is related to MSM0271 but self-organizes as linear strips that may line the facet edge; here, the presence of a novel extendable loop may help ameliorate poor packing geometry of the rigid main particle at the angled edges. In contrast to previously characterized homologs, both of these proteins show closed pores at both ends. This suggests a model where key interactions at the vertex and edges are mediated at the inner layer of the shell by MSM0271 (encircling MSM0273) and MSM0275, and the facet is built from MSM0272 hexamers tiling in the outer layer of the shell.
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Affiliation(s)
- Evan Mallette
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Matthew S Kimber
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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39
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Wagner HJ, Capitain CC, Richter K, Nessling M, Mampel J. Engineering bacterial microcompartments with heterologous enzyme cargos. Eng Life Sci 2016; 17:36-46. [PMID: 32624727 DOI: 10.1002/elsc.201600107] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/16/2016] [Accepted: 07/12/2016] [Indexed: 01/01/2023] Open
Abstract
Bacterial microcompartments (BMCs) are intracellular proteinaceous organelles devoid of a lipid membrane that encapsulates enzymes of metabolic pathways. Salmonella enterica synthesizes propanediol-utilization BMCs containing enzymes involved in the degradation of 1,2-propanediol. BMCs can be designed to enclose heterologous proteins, paving the way to engineered catalytic microreactors. Here, we investigate broader applicability of this design principle by directing three different enzymes to the BMC. We demonstrate that β-galactosidase, esterase Est5, and cofactor-dependent glycerol dehydrogenase can be directed to the BMC and copurified with the microcompartment shell in a catalytically active form. We show that the BMC shell protects enzymes from pH-dependent but not from temperature stress. Moreover, we provide evidence that the heterologously expressed BMCs act as a moderately selective diffusion barrier for lipophilic small molecules.
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Affiliation(s)
- Hanna J Wagner
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany.,Faculty of Biology and Spemann Graduate School of Biology and Medicine (SGBM) University of Freiburg Freiburg Germany
| | - Charlotte C Capitain
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany.,Department of Biotechnology Mannheim University of Applied Sciences Mannheim Germany
| | - Karsten Richter
- German Cancer Research Centre (DKFZ) Core Facility Electron Microscopy (W230) Heidelberg Germany
| | - Michelle Nessling
- German Cancer Research Centre (DKFZ) Core Facility Electron Microscopy (W230) Heidelberg Germany
| | - Jörg Mampel
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany
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40
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Chowdhury C, Chun S, Sawaya MR, Yeates TO, Bobik TA. The function of the PduJ microcompartment shell protein is determined by the genomic position of its encoding gene. Mol Microbiol 2016; 101:770-83. [PMID: 27561553 PMCID: PMC5003431 DOI: 10.1111/mmi.13423] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2016] [Indexed: 12/20/2022]
Abstract
Bacterial microcompartments (MCPs) are complex organelles that consist of metabolic enzymes encapsulated within a protein shell. In this study, we investigate the function of the PduJ MCP shell protein. PduJ is 80% identical in amino acid sequence to PduA and both are major shell proteins of the 1,2-propanediol (1,2-PD) utilization (Pdu) MCP of Salmonella. Prior studies showed that PduA mediates the transport of 1,2-PD (the substrate) into the Pdu MCP. Surprisingly, however, results presented here establish that PduJ has no role 1,2-PD transport. The crystal structure revealed that PduJ was nearly identical to that of PduA and, hence, offered no explanation for their differential functions. Interestingly, however, when a pduJ gene was placed at the pduA chromosomal locus, the PduJ protein acquired a new function, the ability to mediate 1,2-PD transport into the Pdu MCP. To our knowledge, these are the first studies to show that that gene location can determine the function of a MCP shell protein. We propose that gene location dictates protein-protein interactions essential to the function of the MCP shell.
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Affiliation(s)
- Chiranjit Chowdhury
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
| | - Sunny Chun
- Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095
| | - Michael R. Sawaya
- Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095
| | - Todd O. Yeates
- Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
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41
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Held M, Kolb A, Perdue S, Hsu SY, Bloch SE, Quin MB, Schmidt-Dannert C. Engineering formation of multiple recombinant Eut protein nanocompartments in E. coli. Sci Rep 2016; 6:24359. [PMID: 27063436 PMCID: PMC4827028 DOI: 10.1038/srep24359] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/29/2016] [Indexed: 01/17/2023] Open
Abstract
Compartmentalization of designed metabolic pathways within protein based nanocompartments has the potential to increase reaction efficiency in multi-step biosynthetic reactions. We previously demonstrated proof-of-concept of this aim by targeting a functional enzyme to single cellular protein nanocompartments, which were formed upon recombinant expression of the Salmonella enterica LT2 ethanolamine utilization bacterial microcompartment shell proteins EutS or EutSMNLK in Escherichia coli. To optimize this system, increasing overall encapsulated enzyme reaction efficiency, factor(s) required for the production of more than one nanocompartment per cell must be identified. In this work we report that the cupin domain protein EutQ is required for assembly of more than one nanocompartment per cell. Overexpression of EutQ results in multiple nanocompartment assembly in our recombinant system. EutQ specifically interacts with the shell protein EutM in vitro via electrostatic interactions with the putative cytosolic face of EutM. These findings lead to the theory that EutQ could facilitate multiple nanocompartment biogenesis by serving as an assembly hub for shell proteins. This work offers insights into the biogenesis of Eut bacterial microcompartments, and also provides an improved platform for the production of protein based nanocompartments for targeted encapsulation of enzyme pathways.
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Affiliation(s)
- Mark Held
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Alexander Kolb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Sarah Perdue
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Szu-Yi Hsu
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Sarah E Bloch
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Maureen B Quin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
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42
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Jorda J, Leibly DJ, Thompson MC, Yeates TO. Structure of a novel 13 nm dodecahedral nanocage assembled from a redesigned bacterial microcompartment shell protein. Chem Commun (Camb) 2016; 52:5041-4. [PMID: 26988700 DOI: 10.1039/c6cc00851h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the crystal structure of a novel 60-subunit dodecahedral cage that results from self-assembly of a re-engineered version of a natural protein (PduA) from the Pdu microcompartment shell. Biophysical data illustrate the dependence of assembly on solution conditions, opening up new applications in microcompartment studies and nanotechnology.
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Affiliation(s)
- J Jorda
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.
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43
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Bobik TA, Lehman BP, Yeates TO. Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways. Mol Microbiol 2015; 98:193-207. [PMID: 26148529 PMCID: PMC4718714 DOI: 10.1111/mmi.13117] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2015] [Indexed: 12/15/2022]
Abstract
Prokaryotes use subcellular compartments for a variety of purposes. An intriguing example is a family of complex subcellular organelles known as bacterial microcompartments (MCPs). MCPs are widely distributed among bacteria and impact processes ranging from global carbon fixation to enteric pathogenesis. Overall, MCPs consist of metabolic enzymes encased within a protein shell, and their function is to optimize biochemical pathways by confining toxic or volatile metabolic intermediates. MCPs are fundamentally different from other organelles in having a complex protein shell rather than a lipid-based membrane as an outer barrier. This unusual feature raises basic questions about organelle assembly, protein targeting and metabolite transport. In this review, we discuss the three best-studied MCPs highlighting atomic-level models for shell assembly, targeting sequences that direct enzyme encapsulation, multivalent proteins that organize the lumen enzymes, the principles of metabolite movement across the shell, internal cofactor recycling, a potential system of allosteric regulation of metabolite transport and the mechanism and rationale behind the functional diversification of the proteins that form the shell. We also touch on some potential biotechnology applications of an unusual compartment designed by nature to optimize metabolic processes within a cellular context.
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Affiliation(s)
- Thomas A. Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
| | - Brent P. Lehman
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
| | - Todd O. Yeates
- Molecular Biology Institute, University of California, Los Angeles
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles
- Department of Chemistry and Biochemistry, University of California, Los Angeles
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44
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Bioinformatic characterization of glycyl radical enzyme-associated bacterial microcompartments. Appl Environ Microbiol 2015; 81:8315-29. [PMID: 26407889 DOI: 10.1128/aem.02587-15] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 09/18/2015] [Indexed: 12/26/2022] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles encapsulating enzymes that catalyze sequential reactions of metabolic pathways. BMCs are phylogenetically widespread; however, only a few BMCs have been experimentally characterized. Among them are the carboxysomes and the propanediol- and ethanolamine-utilizing microcompartments, which play diverse metabolic and ecological roles. The substrate of a BMC is defined by its signature enzyme. In catabolic BMCs, this enzyme typically generates an aldehyde. Recently, it was shown that the most prevalent signature enzymes encoded by BMC loci are glycyl radical enzymes, yet little is known about the function of these BMCs. Here we characterize the glycyl radical enzyme-associated microcompartment (GRM) loci using a combination of bioinformatic analyses and active-site and structural modeling to show that the GRMs comprise five subtypes. We predict distinct functions for the GRMs, including the degradation of choline, propanediol, and fuculose phosphate. This is the first family of BMCs for which identification of the signature enzyme is insufficient for predicting function. The distinct GRM functions are also reflected in differences in shell composition and apparently different assembly pathways. The GRMs are the counterparts of the vitamin B12-dependent propanediol- and ethanolamine-utilizing BMCs, which are frequently associated with virulence. This study provides a comprehensive foundation for experimental investigations of the diverse roles of GRMs. Understanding this plasticity of function within a single BMC family, including characterization of differences in permeability and assembly, can inform approaches to BMC bioengineering and the design of therapeutics.
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45
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In Salmonella enterica, Ethanolamine Utilization Is Repressed by 1,2-Propanediol To Prevent Detrimental Mixing of Components of Two Different Bacterial Microcompartments. J Bacteriol 2015; 197:2412-21. [PMID: 25962913 DOI: 10.1128/jb.00215-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 04/22/2015] [Indexed: 01/05/2023] Open
Abstract
UNLABELLED Bacterial microcompartments (MCPs) are a diverse family of protein-based organelles composed of metabolic enzymes encapsulated within a protein shell. The function of bacterial MCPs is to optimize metabolic pathways by confining toxic and/or volatile metabolic intermediates. About 20% of bacteria produce MCPs, and there are at least seven different types. Different MCPs vary in their encapsulated enzymes, but all have outer shells composed of highly conserved proteins containing bacterial microcompartment domains. Many organisms have genes encoding more than one type of MCP, but given the high homology among shell proteins, it is uncertain whether multiple MCPs can be functionally expressed in the same cell at the same time. In these studies, we examine the regulation of the 1,2-propanediol (1,2-PD) utilization (Pdu) and ethanolamine utilization (Eut) MCPs in Salmonella. Studies showed that 1,2-PD (shown to induce the Pdu MCP) represses transcription of the Eut MCP and that the PocR regulatory protein is required. The results indicate that repression of the Eut MCP by 1,2-PD is needed to prevent detrimental mixing of shell proteins from the Eut and Pdu MCPs. Coexpression of both MCPs impaired the function of the Pdu MCP and resulted in the formation of hybrid MCPs composed of Eut and Pdu MCP components. We also show that plasmid-based expression of individual shell proteins from the Eut MCP or the β-carboxysome impaired the function of Pdu MCP. Thus, the high conservation among bacterial microcompartment (BMC) domain shell proteins is problematic for coexpression of the Eut and Pdu MCPs and perhaps other MCPs as well. IMPORTANCE Bacterial MCPs are encoded by nearly 20% of bacterial genomes, and almost 40% of those genomes contain multiple MCP gene clusters. In this study, we examine how the regulation of two different MCP systems (Eut and Pdu) is integrated in Salmonella. Our findings indicate that 1,2-PD (shown to induce the Pdu MCP) represses the Eut MCP to prevent detrimental mixing of Eut and Pdu shell proteins. These findings suggest that numerous organisms which produce more than one type of MCP likely need some mechanism to prevent aberrant shell protein interactions.
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46
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Cai F, Sutter M, Bernstein SL, Kinney JN, Kerfeld CA. Engineering bacterial microcompartment shells: chimeric shell proteins and chimeric carboxysome shells. ACS Synth Biol 2015; 4:444-53. [PMID: 25117559 DOI: 10.1021/sb500226j] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacterial microcompartments (BMCs) are self-assembling organelles composed entirely of protein. Depending on the enzymes they encapsulate, BMCs function in either inorganic carbon fixation (carboxysomes) or organic carbon utilization (metabolosomes). The hallmark feature of all BMCs is a selectively permeable shell formed by multiple paralogous proteins, each proposed to confer specific flux characteristics. Gene clusters encoding diverse BMCs are distributed broadly across bacterial phyla, providing a rich variety of building blocks with a predicted range of permeability properties. In theory, shell permeability can be engineered by modifying residues flanking the pores (symmetry axes) of hexameric shell proteins or by combining shell proteins from different types of BMCs into chimeric shells. We undertook both approaches to altering shell properties using the carboxysome as a model system. There are two types of carboxysomes, α and β. In both, the predominant shell protein(s) contain a single copy of the BMC domain (pfam00936), but they are significantly different in primary structure. Indeed, phylogenetic analysis shows that the two types of carboxysome shell proteins are more similar to their counterparts in metabolosomes than to each other. We solved high resolution crystal structures of the major shell proteins, CsoS1 and CcmK2, and the presumed minor shell protein CcmK4, representing both types of cyanobacterial carboxysomes and then tested the interchangeability. The in vivo study presented here confirms that both engineering pores to mimic those of other shell proteins and the construction of chimeric shells is feasible.
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Affiliation(s)
- Fei Cai
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Markus Sutter
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- MSU-DOE
Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
| | - Susan L. Bernstein
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - James N. Kinney
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Cheryl A. Kerfeld
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- MSU-DOE
Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
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47
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Selective molecular transport through the protein shell of a bacterial microcompartment organelle. Proc Natl Acad Sci U S A 2015; 112:2990-5. [PMID: 25713376 DOI: 10.1073/pnas.1423672112] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial microcompartments are widespread prokaryotic organelles that have important and diverse roles ranging from carbon fixation to enteric pathogenesis. Current models for microcompartment function propose that their outer protein shell is selectively permeable to small molecules, but whether a protein shell can mediate selective permeability and how this occurs are unresolved questions. Here, biochemical and physiological studies of structure-guided mutants are used to show that the hexameric PduA shell protein of the 1,2-propanediol utilization (Pdu) microcompartment forms a selectively permeable pore tailored for the influx of 1,2-propanediol (the substrate of the Pdu microcompartment) while restricting the efflux of propionaldehyde, a toxic intermediate of 1,2-propanediol catabolism. Crystal structures of various PduA mutants provide a foundation for interpreting the observed biochemical and phenotypic data in terms of molecular diffusion across the shell. Overall, these studies provide a basis for understanding a class of selectively permeable channels formed by nonmembrane proteins.
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48
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Bacterial microcompartments and the modular construction of microbial metabolism. Trends Microbiol 2015; 23:22-34. [DOI: 10.1016/j.tim.2014.10.003] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/07/2014] [Accepted: 10/08/2014] [Indexed: 01/22/2023]
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49
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Kim EY, Slininger MF, Tullman-Ercek D. The effects of time, temperature, and pH on the stability of PDU bacterial microcompartments. Protein Sci 2014; 23:1434-41. [PMID: 25053115 DOI: 10.1002/pro.2527] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/21/2014] [Accepted: 07/21/2014] [Indexed: 12/18/2022]
Abstract
Bacterial microcompartments (MCPs) are subcellular organelles that are composed of a protein shell and encapsulated metabolic enzymes. It has been suggested that MCPs can be engineered to encapsulate protein cargo for use as in vivo nanobioreactors or carriers for drug delivery. Understanding the stability of the MCP shell is critical for such applications. Here, we investigate the integrity of the propanediol utilization (Pdu) MCP shell of Salmonella enterica over time, in buffers with various pH, and at elevated temperatures. The results show that MCPs are remarkably stable. When stored at 4°C or at room temperature, Pdu MCPs retain their structure for several days, both in vivo and in vitro. Furthermore, Pdu MCPs can tolerate temperatures up to 60°C without apparent structural degradation. MCPs are, however, sensitive to pH and require conditions between pH 6 and pH 10. In nonoptimal conditions, MCPs form aggregates. However, within the aggregated protein mass, MCPs often retain their polyhedral outlines. These results show that MCPs are highly robust, making them suitable for a wide range of applications.
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Affiliation(s)
- Edward Y Kim
- Department of Chemical and Biomolecular Engineering, The University of California, Berkeley, California, 94720
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