1
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Gu S, Bradley-Clarke J, Rose RS, Warren MJ, Pickersgill RW. Enzyme-cargo encapsulation peptides bind between tessellating tiles of the bacterial microcompartment shell. J Biol Chem 2024; 300:107357. [PMID: 38735476 PMCID: PMC11157265 DOI: 10.1016/j.jbc.2024.107357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 04/11/2024] [Accepted: 04/14/2024] [Indexed: 05/14/2024] Open
Abstract
Bacterial microcompartments are prokaryotic organelles comprising encapsulated enzymes within a thin protein shell. They facilitate metabolic processing including propanediol, choline, glycerol, and ethanolamine utilization, and they accelerate carbon fixation in cyanobacteria. Enzymes targeted to the inside of the microcompartment frequently possess a cargo-encapsulation peptide, but the site to which the peptide binds is unclear. We provide evidence that the encapsulation peptides bind to the hydrophobic groove formed between tessellating subunits of the shell proteins. In silico docking studies provide a compelling model of peptide binding to this prominent hydrophobic groove. This result is consistent with the now widely accepted view that the convex side of the shell oligomers faces the lumen of the microcompartment. The binding of the encapsulation peptide to the groove between tessellating shell protein tiles explains why it has been difficult to define the peptide binding site using other methods, provides a mechanism by which encapsulation-peptide bearing enzymes can promote shell assembly, and explains how the presence of cargo affects the size and shape of the bacterial microcompartment. This knowledge may be exploited in engineering microcompartments or disease prevention by hampering cargo encapsulation.
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Affiliation(s)
- Shuang Gu
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, UK
| | - Jack Bradley-Clarke
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, UK
| | - Ruth-Sarah Rose
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Richard W Pickersgill
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, UK.
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2
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Trettel DS, Pacheco SL, Laskie AK, Gonzalez-Esquer CR. Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation. FRONTIERS IN PLANT SCIENCE 2024; 15:1346759. [PMID: 38425792 PMCID: PMC10902431 DOI: 10.3389/fpls.2024.1346759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
The carboxysome is a bacterial microcompartment (BMC) which plays a central role in the cyanobacterial CO2-concentrating mechanism. These proteinaceous structures consist of an outer protein shell that partitions Rubisco and carbonic anhydrase from the rest of the cytosol, thereby providing a favorable microenvironment that enhances carbon fixation. The modular nature of carboxysomal architectures makes them attractive for a variety of biotechnological applications such as carbon capture and utilization. In silico approaches, such as molecular dynamics (MD) simulations, can support future carboxysome redesign efforts by providing new spatio-temporal insights on their structure and function beyond in vivo experimental limitations. However, specific computational studies on carboxysomes are limited. Fortunately, all BMC (including the carboxysome) are highly structurally conserved which allows for practical inferences to be made between classes. Here, we review simulations on BMC architectures which shed light on (1) permeation events through the shell and (2) assembly pathways. These models predict the biophysical properties surrounding the central pore in BMC-H shell subunits, which in turn dictate the efficiency of substrate diffusion. Meanwhile, simulations on BMC assembly demonstrate that assembly pathway is largely dictated kinetically by cargo interactions while final morphology is dependent on shell factors. Overall, these findings are contextualized within the wider experimental BMC literature and framed within the opportunities for carboxysome redesign for biomanufacturing and enhanced carbon fixation.
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Affiliation(s)
- Daniel S. Trettel
- Los Alamos National Laboratory, Bioscience Division, Microbial and Biome Sciences Group, Los Alamos, NM, United States
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3
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Trettel DS, Neale C, Zhao M, Gnanakaran S, Gonzalez-Esquer CR. Monatomic ions influence substrate permeation across bacterial microcompartment shells. Sci Rep 2023; 13:15738. [PMID: 37735196 PMCID: PMC10514305 DOI: 10.1038/s41598-023-42688-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Bacterial microcompartments (BMCs) are protein organelles consisting of an inner enzymatic core encased within a selectively permeable shell. BMC shells are modular, tractable architectures that can be repurposed with new interior enzymes for biomanufacturing purposes. The permeability of BMC shells is function-specific and regulated by biophysical properties of the shell subunits, especially its pores. We hypothesized that ions may interact with pore residues in a manner that influences the substrate permeation process. In vitro activity comparisons between native and broken BMCs demonstrated that increasing NaCl negatively affects permeation rates. Molecular dynamics simulations of the dominant shell protein (BMC-H) revealed that chloride ions preferentially occupy the positive pore, hindering substrate permeation, while sodium cations remain excluded. Overall, these results demonstrate that shell properties influence ion permeability and leverages the integration of experimental and computational techniques to improve our understanding of BMC shells towards their repurposing for biotechnological applications.
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Affiliation(s)
- Daniel S Trettel
- Biosciences Division, Microbial and Biome Sciences Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Chris Neale
- Theoretical Division, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Mingfei Zhao
- Theoretical Division, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - S Gnanakaran
- Theoretical Division, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - C Raul Gonzalez-Esquer
- Biosciences Division, Microbial and Biome Sciences Group, Los Alamos National Laboratory, Los Alamos, NM, USA.
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4
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Waltmann C, Kennedy NW, Mills CE, Roth EW, Ikonomova SP, Tullman-Ercek D, Olvera de la Cruz M. Kinetic Growth of Multicomponent Microcompartment Shells. ACS NANO 2023; 17:15751-15762. [PMID: 37552700 DOI: 10.1021/acsnano.3c03353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Overall, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.
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Affiliation(s)
- Curt Waltmann
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Nolan W Kennedy
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Carolyn E Mills
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Eric W Roth
- Northwestern University Atomic and Nanoscale Characterization Experimentation Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Svetlana P Ikonomova
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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5
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Evans SL, Al-Hazeem MMJ, Mann D, Smetacek N, Beavil AJ, Sun Y, Chen T, Dykes GF, Liu LN, Bergeron JRC. Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact α-carboxysome. Structure 2023; 31:677-688.e4. [PMID: 37015227 PMCID: PMC10689251 DOI: 10.1016/j.str.2023.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/19/2023] [Accepted: 03/09/2023] [Indexed: 04/05/2023]
Abstract
Carboxysomes are proteinaceous bacterial microcompartments that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, encapsulating several enzymes, including ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for the first step of the Calvin-Benson-Bassham cycle. Despite their significance in carbon fixation and great bioengineering potentials, the structural understanding of native carboxysomes is currently limited to low-resolution studies. Here, we report the characterization of a native α-carboxysome from a marine cyanobacterium by single-particle cryoelectron microscopy (cryo-EM). We have determined the structure of its RuBisCO enzyme, and obtained low-resolution maps of its icosahedral shell, and of its concentric interior organization. Using integrative modeling approaches, we have proposed a complete atomic model of an intact carboxysome, providing insight into its organization and assembly. This is critical for a better understanding of the carbon fixation mechanism and toward repurposing carboxysomes in synthetic biology for biotechnological applications.
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Affiliation(s)
- Sasha L Evans
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Monsour M J Al-Hazeem
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daniel Mann
- Ernst-Ruska Centre 3, Forschungszentrum Jülich, Jülich, Germany
| | - Nicolas Smetacek
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - Andrew J Beavil
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, Shandong, China.
| | - Julien R C Bergeron
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK; Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK.
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6
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Chen T, Hojka M, Davey P, Sun Y, Dykes GF, Zhou F, Lawson T, Nixon PJ, Lin Y, Liu LN. Engineering α-carboxysomes into plant chloroplasts to support autotrophic photosynthesis. Nat Commun 2023; 14:2118. [PMID: 37185249 PMCID: PMC10130085 DOI: 10.1038/s41467-023-37490-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/17/2023] [Indexed: 05/17/2023] Open
Abstract
The growth in world population, climate change, and resource scarcity necessitate a sustainable increase in crop productivity. Photosynthesis in major crops is limited by the inefficiency of the key CO2-fixing enzyme Rubisco, owing to its low carboxylation rate and poor ability to discriminate between CO2 and O2. In cyanobacteria and proteobacteria, carboxysomes function as the central CO2-fixing organelles that elevate CO2 levels around encapsulated Rubisco to enhance carboxylation. There is growing interest in engineering carboxysomes into crop chloroplasts as a potential route for improving photosynthesis and crop yields. Here, we generate morphologically correct carboxysomes in tobacco chloroplasts by transforming nine carboxysome genetic components derived from a proteobacterium. The chloroplast-expressed carboxysomes display a structural and functional integrity comparable to native carboxysomes and support autotrophic growth and photosynthesis of the transplastomic plants at elevated CO2. Our study provides proof-of-concept for a route to engineering fully functional CO2-fixing modules and entire CO2-concentrating mechanisms into chloroplasts to improve crop photosynthesis and productivity.
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Affiliation(s)
- Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China
| | - Marta Hojka
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Philip Davey
- School of Life Sciences, University of Essex, Colchester, CO4 4SQ, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Colchester, CO4 4SQ, UK
| | - Peter J Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China.
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 266003, Qingdao, China.
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7
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Trettel DS, Winkler WC. In Vitro Analysis of Bacterial Microcompartments and Shell Protein Superstructures by Confocal Microscopy. Microbiol Spectr 2023; 11:e0335722. [PMID: 36786617 PMCID: PMC10100840 DOI: 10.1128/spectrum.03357-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
The shell proteins that comprise bacterial microcompartments (BMCs) can self-assemble into an array of superstructures such as nanotubes, flat sheets, and icosahedra. The physical characterization of BMCs and these superstructures typically relies on electron microscopy, which decouples samples from their solution context. We hypothesize that an investigation of fluorescently tagged BMCs and shell protein superstructures in vitro using high-resolution confocal microscopy will lead to new insights into the solution behavior of these entities. We find that confocal imaging is able to capture nanotubes and sheets previously reported by transmission electron microscopy (TEM). Using a combination of fluorescent tags, we present qualitative evidence that these structures intermix with one another in a hetero- and homotypic fashion. Complete BMCs are also able to accomplish intermixing as evidenced by colocalization data. Finally, a simple colocalization experiment suggests that fluorescently modified encapsulation peptides (EPs) may prefer certain shell protein binding partners. Together, these data demonstrate that high-resolution confocal microscopy is a powerful tool for investigating microcompartment-related structures in vitro, particularly for colocalization analyses. These results also support the notion that BMCs may intermix protein components, presumably from the outer shell. IMPORTANCE Microcompartments are large, organelle-like structures that help bacteria catabolize targeted metabolites while also protecting the cytosol against highly reactive metabolic intermediates. Their protein shell self-assembles into a polyhedral structure of approximately 100 to 200 nm in diameter. Inside the shell are thousands of copies of cargo enzymes, which are responsible for a specific metabolic pathway. While different approaches have revealed high-resolution structures of individual microcompartment proteins, it is less clear how these factors self-assemble to form the full native structure. In this study, we show that laser scanning confocal microscopy can be used to study microcompartment proteins. We find that this approach allows researchers to investigate the interactions and potential exchange of shell protein subunits in solution. From this, we conclude that confocal microscopy offers advantages for studying the in vitro structures of other microcompartments as well as carboxysomes and other bacterial organelles.
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Affiliation(s)
- Daniel S. Trettel
- Department of Chemistry and Biochemistry, The University of Maryland, College Park, College Park, Maryland, USA
| | - Wade C. Winkler
- Department of Chemistry and Biochemistry, The University of Maryland, College Park, College Park, Maryland, USA
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, College Park, Maryland, USA
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8
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Rusilowicz M, Newman DW, Creamer DR, Johnson J, Adair K, Harman VM, Grant CM, Beynon RJ, Hubbard SJ. AlacatDesigner─Computational Design of Peptide Concatamers for Protein Quantitation. J Proteome Res 2023; 22:594-604. [PMID: 36688735 PMCID: PMC9903321 DOI: 10.1021/acs.jproteome.2c00608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protein quantitation via mass spectrometry relies on peptide proxies for the parent protein from which abundances are estimated. Owing to the variability in signal from individual peptides, accurate absolute quantitation usually relies on the addition of an external standard. Typically, this involves stable isotope-labeled peptides, delivered singly or as a concatenated recombinant protein. Consequently, the selection of the most appropriate surrogate peptides and the attendant design in recombinant proteins termed QconCATs are challenges for proteome science. QconCATs can now be built in a "a-la-carte" assembly method using synthetic biology: ALACATs. To assist their design, we present "AlacatDesigner", a tool that supports the peptide selection for recombinant protein standards based on the user's target protein. The user-customizable tool considers existing databases, occurrence in the literature, potential post-translational modifications, predicted miscleavage, predicted divergence of the peptide and protein quantifications, and ionization potential within the mass spectrometer. We show that peptide selections are enriched for good proteotypic and quantotypic candidates compared to empirical data. The software is freely available to use either via a web interface AlacatDesigner, downloaded as a Desktop application or imported as a Python package for the command line interface or in scripts.
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Affiliation(s)
- Martin Rusilowicz
- Division
of Evolution, Infection and Genomics, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - David W. Newman
- Division
of Evolution, Infection and Genomics, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Declan R. Creamer
- Division
of Molecular and Cellular Function, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - James Johnson
- GeneMill,
Institute of Systems Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United
Kingdom
| | - Kareena Adair
- Centre
for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United
Kingdom
| | - Victoria M. Harman
- Centre
for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United
Kingdom
| | - Chris M. Grant
- Division
of Molecular and Cellular Function, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Robert J. Beynon
- Centre
for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United
Kingdom
| | - Simon J. Hubbard
- Division
of Evolution, Infection and Genomics, School of Biological Sciences,
Faculty of Biology, Medicine and Health, Manchester Academic Health
Science Centre, University of Manchester, Manchester M13 9PT, United Kingdom,
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9
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Getting the Payload in Place - Unravelling the Complexities of Making a Bacterial Microcompartment. J Bacteriol 2022; 204:e0012722. [PMID: 36000835 PMCID: PMC9487458 DOI: 10.1128/jb.00127-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial microcompartments (BMCs) are complex macromolecular assemblies composed of any outer protein shell that encases a specific metabolic pathway cargo. Recent research is now starting to unravel some of the processes that are involved in directing the enzyme cargo to the inside of the BMC. In particular, an article in this issue of J Bacteriol by N. W. Kennedy, C. E. Mills, C. H. Abrahamson, A. Archer, et al. (J Bacteriol 204:e00576-21, 2022, https://doi.org/10.1128/jb.00576-21) highlights the role played by the shell protein PduB in coordinating this internalization process.
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10
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Huang J, Jiang Q, Yang M, Dykes GF, Weetman SL, Xin W, He HL, Liu LN. Probing the Internal pH and Permeability of a Carboxysome Shell. Biomacromolecules 2022; 23:4339-4348. [PMID: 36054822 PMCID: PMC9554877 DOI: 10.1021/acs.biomac.2c00781] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The carboxysome is a protein-based nanoscale organelle
in cyanobacteria
and many proteobacteria, which encapsulates the key CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)
and carbonic anhydrase (CA) within a polyhedral protein shell. The
intrinsic self-assembly and architectural features of carboxysomes
and the semipermeability of the protein shell provide the foundation
for the accumulation of CO2 within carboxysomes and enhanced
carboxylation. Here, we develop an approach to determine the interior
pH conditions and inorganic carbon accumulation within an α-carboxysome
shell derived from a chemoautotrophic proteobacterium Halothiobacillus neapolitanus and evaluate the shell
permeability. By incorporating a pH reporter, pHluorin2, within empty
α-carboxysome shells produced in Escherichia
coli, we probe the interior pH of the protein shells
with and without CA. Our in vivo and in vitro results demonstrate a lower interior pH of α-carboxysome shells
than the cytoplasmic pH and buffer pH, as well as the modulation of
the interior pH in response to changes in external environments, indicating
the shell permeability to bicarbonate ions and protons. We further
determine the saturated HCO3– concentration
of 15 mM within α-carboxysome shells and show the CA-mediated
increase in the interior CO2 level. Uncovering the interior
physiochemical microenvironment of carboxysomes is crucial for understanding
the mechanisms underlying carboxysomal shell permeability and enhancement
of Rubisco carboxylation within carboxysomes. Such fundamental knowledge
may inform reprogramming carboxysomes to improve metabolism and recruit
foreign enzymes for enhanced catalytical performance.
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Affiliation(s)
- Jiafeng Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,School of Life Sciences, Central South University, Changsha 410017, China
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Mengru Yang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Samantha L Weetman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Wei Xin
- Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 271000, China
| | - Hai-Lun He
- School of Life Sciences, Central South University, Changsha 410017, China
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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11
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Mills CE, Waltmann C, Archer AG, Kennedy NW, Abrahamson CH, Jackson AD, Roth EW, Shirman S, Jewett MC, Mangan NM, Olvera de la Cruz M, Tullman-Ercek D. Vertex protein PduN tunes encapsulated pathway performance by dictating bacterial metabolosome morphology. Nat Commun 2022; 13:3746. [PMID: 35768404 PMCID: PMC9243111 DOI: 10.1038/s41467-022-31279-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 06/09/2022] [Indexed: 11/09/2022] Open
Abstract
Engineering subcellular organization in microbes shows great promise in addressing bottlenecks in metabolic engineering efforts; however, rules guiding selection of an organization strategy or platform are lacking. Here, we study compartment morphology as a factor in mediating encapsulated pathway performance. Using the 1,2-propanediol utilization microcompartment (Pdu MCP) system from Salmonella enterica serovar Typhimurium LT2, we find that we can shift the morphology of this protein nanoreactor from polyhedral to tubular by removing vertex protein PduN. Analysis of the metabolic function between these Pdu microtubes (MTs) shows that they provide a diffusional barrier capable of shielding the cytosol from a toxic pathway intermediate, similar to native MCPs. However, kinetic modeling suggests that the different surface area to volume ratios of MCP and MT structures alters encapsulated pathway performance. Finally, we report a microscopy-based assay that permits rapid assessment of Pdu MT formation to enable future engineering efforts on these structures. Morphology of metabolosomes affects the encapsulated pathway performance. Here, the authors combine experimental characterizations with structural and kinetic modeling to reveal how the shell protein PduN changes the morphology of 1,2-propanediol utilization (Pdu) metabolosome and how this morphology shift impacts Pdu function.
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Affiliation(s)
- Carolyn E Mills
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Curt Waltmann
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA
| | - Andre G Archer
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA
| | - Nolan W Kennedy
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Charlotte H Abrahamson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Alexander D Jackson
- Master of Science in Biotechnology Program, Northwestern University, Evanston, IL, USA
| | - Eric W Roth
- Northwestern University Atomic and Nanoscale Characterization Experimental Center, Evanston, IL, USA
| | - Sasha Shirman
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Niall M Mangan
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.,Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA. .,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
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12
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The roles of diol dehydratase from pdu operon on glycerol catabolism in Klebsiella pneumoniae. Enzyme Microb Technol 2022; 157:110021. [DOI: 10.1016/j.enzmictec.2022.110021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/24/2022] [Accepted: 02/21/2022] [Indexed: 11/23/2022]
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13
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Linking the Salmonella enterica 1,2-Propanediol Utilization Bacterial Microcompartment Shell to the Enzymatic Core via the Shell Protein PduB. J Bacteriol 2022; 204:e0057621. [PMID: 35575582 DOI: 10.1128/jb.00576-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Bacterial microcompartments (MCPs) are protein-based organelles that house the enzymatic machinery for metabolism of niche carbon sources, allowing enteric pathogens to outcompete native microbiota during host colonization. While much progress has been made toward understanding MCP biogenesis, questions still remain regarding the mechanism by which core MCP enzymes are enveloped within the MCP protein shell. Here, we explore the hypothesis that the shell protein PduB is responsible for linking the shell of the 1,2-propanediol utilization (Pdu) MCP from Salmonella enterica serovar Typhimurium LT2 to its enzymatic core. Using fluorescent reporters, we demonstrate that all members of the Pdu enzymatic core are encapsulated in Pdu MCPs. We also demonstrate that PduB is critical for linking the entire Pdu enzyme core to the MCP shell. Using MCP purifications, transmission electron microscopy, and fluorescence microscopy, we find that shell assembly can be decoupled from the enzymatic core, as apparently empty MCPs are formed in Salmonella strains lacking PduB. Mutagenesis studies reveal that PduB is incorporated into the Pdu MCP shell via a conserved, lysine-mediated hydrogen bonding mechanism. Finally, growth assays and system-level pathway modeling reveal that unencapsulated pathway performance is strongly impacted by enzyme concentration, highlighting the importance of minimizing polar effects when conducting these functional assays. Together, these results provide insight into the mechanism of enzyme encapsulation within Pdu MCPs and demonstrate that the process of enzyme encapsulation and shell assembly are separate processes in this system, a finding that will aid future efforts to understand MCP biogenesis. IMPORTANCE MCPs are unique, genetically encoded organelles used by many bacteria to survive in resource-limited environments. There is significant interest in understanding the biogenesis and function of these organelles, both as potential antibiotic targets in enteric pathogens and also as useful tools for overcoming metabolic engineering bottlenecks. However, the mechanism by which these organelles are formed natively is still not completely understood. Here, we provide evidence of a potential mechanism in S. enterica by which a single protein, PduB, links the MCP shell and metabolic core. This finding is critical for those seeking to disrupt MCPs during pathogenic infections or for those seeking to harness MCPs as nanobioreactors in industrial settings.
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14
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Abstract
Carboxysomes are anabolic bacterial microcompartments that play an essential role in carbon fixation in cyanobacteria and some chemoautotrophs. This self-assembling organelle encapsulates the key CO2-fixing enzymes, Rubisco, and carbonic anhydrase using a polyhedral protein shell that is constructed by hundreds of shell protein paralogs. The α-carboxysome from the chemoautotroph Halothiobacillus neapolitanus serves as a model system in fundamental studies and synthetic engineering of carboxysomes. In this study, we adopted a QconCAT-based quantitative mass spectrometry approach to determine the stoichiometric composition of native α-carboxysomes from H. neapolitanus. We further performed an in-depth comparison of the protein stoichiometry of native α-carboxysomes and their recombinant counterparts heterologously generated in Escherichia coli to evaluate the structural variability and remodeling of α-carboxysomes. Our results provide insight into the molecular principles that mediate carboxysome assembly, which may aid in rational design and reprogramming of carboxysomes in new contexts for biotechnological applications. IMPORTANCE A wide range of bacteria use special protein-based organelles, termed bacterial microcompartments, to encase enzymes and reactions to increase the efficiency of biological processes. As a model bacterial microcompartment, the carboxysome contains a protein shell filled with the primary carbon fixation enzyme Rubisco. The self-assembling organelle is generated by hundreds of proteins and plays important roles in converting carbon dioxide to sugar, a process known as carbon fixation. In this study, we uncovered the exact stoichiometry of all building components and the structural plasticity of the functional α-carboxysome, using newly developed quantitative mass spectrometry together with biochemistry, electron microscopy, and enzymatic assay. The study advances our understanding of the architecture and modularity of natural carboxysomes. The knowledge learned from natural carboxysomes will suggest feasible ways to produce functional carboxysomes in other hosts, such as crop plants, with the overwhelming goal of boosting cell metabolism and crop yields.
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15
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Trettel DS, Resager W, Ueberheide BM, Jenkins CC, Winkler WC. Chemical probing provides insight into the native assembly state of a bacterial microcompartment. Structure 2022; 30:537-550.e5. [PMID: 35216657 PMCID: PMC8995372 DOI: 10.1016/j.str.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/08/2021] [Accepted: 01/28/2022] [Indexed: 11/28/2022]
Abstract
Bacterial microcompartments (BMCs) are widespread in bacteria and are used for a variety of metabolic purposes, including catabolism of host metabolites. A suite of proteins self-assembles into the shell and cargo layers of BMCs. However, the native assembly state of these large complexes remains to be elucidated. Herein, chemical probes were used to observe structural features of a native BMC. While the exterior could be demarcated with fluorophores, the interior was unexpectedly permeable, suggesting that the shell layer may be more dynamic than previously thought. This allowed access to cross-linking chemical probes, which were analyzed to uncover the protein interactome. These cross-links revealed a complex multivalent network among cargo proteins that contained encapsulation peptides and demonstrated that the shell layer follows discrete rules in its assembly. These results are consistent overall with a model in which biomolecular condensation drives interactions of cargo proteins before envelopment by shell layer proteins.
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Affiliation(s)
- Daniel S Trettel
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - William Resager
- New York University Grossman School of Health, NYU Langone Health, New York, NY 10016, USA
| | - Beatrix M Ueberheide
- New York University Grossman School of Health, NYU Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neurology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Conor C Jenkins
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Wade C Winkler
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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16
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Chen T, Fang Y, Jiang Q, Dykes GF, Lin Y, Price GD, Long BM, Liu LN. Incorporation of Functional Rubisco Activases into Engineered Carboxysomes to Enhance Carbon Fixation. ACS Synth Biol 2022; 11:154-161. [PMID: 34664944 PMCID: PMC8787814 DOI: 10.1021/acssynbio.1c00311] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
The carboxysome is
a versatile paradigm of prokaryotic organelles
and is a proteinaceous self-assembling microcompartment that plays
essential roles in carbon fixation in all cyanobacteria and some chemoautotrophs.
The carboxysome encapsulates
the central CO2-fixing enzyme, ribulose-1,5-bisphosphate
carboxylase/oxygenase (Rubisco), using a polyhedral protein shell
that is selectively permeable to specific metabolites in favor of
Rubisco carboxylation. There is tremendous interest in repurposing
carboxysomes to boost carbon fixation in heterologous organisms. Here,
we develop the design and engineering of α-carboxysomes by coexpressing
the Rubisco activase components CbbQ and CbbO with α-carboxysomes
in Escherichia coli. Our results show
that CbbQ and CbbO could assemble into the reconstituted α-carboxysome
as intrinsic components. Incorporation of both CbbQ and CbbO within
the carboxysome promotes activation of Rubisco and enhances the CO2-fixation activities of recombinant carboxysomes. We also
show that the structural composition of these carboxysomes could be
modified in different expression systems, representing the plasticity
of the carboxysome architecture. In translational terms, our study
informs strategies for engineering and modulating carboxysomes in
diverse biotechnological applications.
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Affiliation(s)
- Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Fang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Gregory F. Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - G. Dean Price
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory 2601, Australia
| | - Benedict M. Long
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory 2601, Australia
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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17
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Liu LN. Advances in the bacterial organelles for CO 2 fixation. Trends Microbiol 2021; 30:567-580. [PMID: 34802870 DOI: 10.1016/j.tim.2021.10.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 02/08/2023]
Abstract
Carboxysomes are a family of bacterial microcompartments (BMCs), present in all cyanobacteria and some proteobacteria, which encapsulate the primary CO2-fixing enzyme, Rubisco, within a virus-like polyhedral protein shell. Carboxysomes provide significantly elevated levels of CO2 around Rubisco to maximize carboxylation and reduce wasteful photorespiration, thus functioning as the central CO2-fixation organelles of bacterial CO2-concentration mechanisms. Their intriguing architectural features allow carboxysomes to make a vast contribution to carbon assimilation on a global scale. In this review, we discuss recent research progress that provides new insights into the mechanisms of how carboxysomes are assembled and functionally maintained in bacteria and recent advances in synthetic biology to repurpose the metabolic module in diverse applications.
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Affiliation(s)
- Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 266003 Qingdao, China.
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18
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Li S, Matoz-Fernandez DA, Olvera de la Cruz M. Effect of Mechanical Properties on Multicomponent Shell Patterning. ACS NANO 2021; 15:14804-14812. [PMID: 34402621 DOI: 10.1021/acsnano.1c04795] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Self-organized shells are fundamental in biological compartmentalization. They protect genomic material or enclose enzymes to aid the metabolic process. Studies of crystalline shells have shown the importance of the mechanical properties of building units in the shell morphology. However, the mechanism underlying the morphology of multicomponent assemblies is still poorly understood. Here, we analyze multicomponent closed shells that have different mechanical properties. By minimizing elastic energy, we show that heterogeneous bending rigidities regulate the surface pattern into circular, spikes, and ridge shapes. Interestingly, our continuum elasticity model recovers the patterns that have been proposed in bacterial microcompartments (BMCs), which are self-organized protein shells that aid the breakdown of complex molecules and allow bacteria to survive in hostile environments. In addition, our work elucidates the principles of pattern formation that can be used to design and engineer multicomponent microcompartments with a specific surface distribution of the components.
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Affiliation(s)
- Siyu Li
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, United States
| | - Daniel A Matoz-Fernandez
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, United States
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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19
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Johnson J, Harman VM, Franco C, Emmott E, Rockliffe N, Sun Y, Liu LN, Takemori A, Takemori N, Beynon RJ. Construction of à la carte QconCAT protein standards for multiplexed quantification of user-specified target proteins. BMC Biol 2021; 19:195. [PMID: 34496840 PMCID: PMC8425055 DOI: 10.1186/s12915-021-01135-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/28/2021] [Indexed: 11/17/2022] Open
Abstract
Background QconCATs are quantitative concatamers for proteomic applications that yield stoichiometric quantities of sets of stable isotope-labelled internal standards. However, changing a QconCAT design, for example, to replace poorly performing peptide standards has been a protracted process. Results We report a new approach to the assembly and construction of QconCATs, based on synthetic biology precepts of biobricks, making use of loop assembly to construct larger entities from individual biobricks. The basic building block (a Qbrick) is a segment of DNA that encodes two or more quantification peptides for a single protein, readily held in a repository as a library resource. These Qbricks are then assembled in a one tube ligation reaction that enforces the order of assembly, to yield short QconCATs that are useable for small quantification products. However, the DNA context of the short construct also allows a second cycle of loop assembly such that five different short QconCATs can be assembled into a longer QconCAT in a second, single tube ligation. From a library of Qbricks, a bespoke QconCAT can be assembled quickly and efficiently in a form suitable for expression and labelling in vivo or in vitro. Conclusions We refer to this approach as the ALACAT strategy as it permits à la carte design of quantification standards. ALACAT methodology is a major gain in flexibility of QconCAT implementation as it supports rapid editing and improvement of QconCATs and permits, for example, substitution of one peptide by another. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01135-9.
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Affiliation(s)
- James Johnson
- GeneMill, Institute of Systems Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Victoria M Harman
- Centre for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, UK
| | - Catarina Franco
- Centre for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, UK
| | - Edward Emmott
- Centre for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, UK
| | - Nichola Rockliffe
- GeneMill, Institute of Systems Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, UK
| | - Ayako Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Shitsukawa, Toon, Ehime, Japan
| | - Nobuaki Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Shitsukawa, Toon, Ehime, Japan
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Systems and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, UK.
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20
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Bobik TA, Stewart AM. Selective molecular transport across the protein shells of bacterial microcompartments. Curr Opin Microbiol 2021; 62:76-83. [PMID: 34087617 PMCID: PMC8286307 DOI: 10.1016/j.mib.2021.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/20/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022]
Abstract
Bacterial microcompartments are widespread organelles that play important roles in the environment and are associated with a number of human diseases. A key feature of bacterial MCPs is a selectively permeable protein shell that mediates the movement of substrates, products and cofactors in and out. Here we discuss current knowledge of selective transport across the protein shells of bacterial MCPs, including mechanisms, regulation and unanswered questions.
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Affiliation(s)
- Thomas A Bobik
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - Andrew M Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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21
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Huokko T, Ni T, Dykes GF, Simpson DM, Brownridge P, Conradi FD, Beynon RJ, Nixon PJ, Mullineaux CW, Zhang P, Liu LN. Probing the biogenesis pathway and dynamics of thylakoid membranes. Nat Commun 2021; 12:3475. [PMID: 34108457 PMCID: PMC8190092 DOI: 10.1038/s41467-021-23680-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 05/11/2021] [Indexed: 01/30/2023] Open
Abstract
How thylakoid membranes are generated to form a metabolically active membrane network and how thylakoid membranes orchestrate the insertion and localization of protein complexes for efficient electron flux remain elusive. Here, we develop a method to modulate thylakoid biogenesis in the rod-shaped cyanobacterium Synechococcus elongatus PCC 7942 by modulating light intensity during cell growth, and probe the spatial-temporal stepwise biogenesis process of thylakoid membranes in cells. Our results reveal that the plasma membrane and regularly arranged concentric thylakoid layers have no physical connections. The newly synthesized thylakoid membrane fragments emerge between the plasma membrane and pre-existing thylakoids. Photosystem I monomers appear in the thylakoid membranes earlier than other mature photosystem assemblies, followed by generation of Photosystem I trimers and Photosystem II complexes. Redistribution of photosynthetic complexes during thylakoid biogenesis ensures establishment of the spatial organization of the functional thylakoid network. This study provides insights into the dynamic biogenesis process and maturation of the functional photosynthetic machinery.
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Affiliation(s)
- Tuomas Huokko
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Tao Ni
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Deborah M Simpson
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Philip Brownridge
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Fabian D Conradi
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Robert J Beynon
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Peter J Nixon
- Department of Life Sciences, Imperial College London, London, UK
| | - Conrad W Mullineaux
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
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22
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Chen H, Wilson J, Ottinger S, Gan Q, Fan C. Introducing noncanonical amino acids for studying and engineering bacterial microcompartments. Curr Opin Microbiol 2021; 61:67-72. [PMID: 33813159 PMCID: PMC8169543 DOI: 10.1016/j.mib.2021.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/28/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
Bacterial microcompartments (BMCs) with selectively permeable shells and encapsulated enzyme cores are well-suited candidates for nano-bioreactors because of their advantages of enhancing pathway flux and protection against toxic products. To better study and engineer protein-based BMCs, a series of protein chemistry approaches are adopted. As one of the most advanced techniques, genetic code expansion can introduce various noncanonical amino acids (ncAAs) with diverse functional groups into target proteins, thus providing powerful tools for protein studies and engineering. This review summarizes and proposes useful tools based on current development of the genetic code expansion technique towards challenges in BMC studies and engineering.
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Affiliation(s)
- Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA
| | - Jessica Wilson
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA
| | - Sara Ottinger
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA; Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA.
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23
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Rodríguez JM, Allende-Ballestero C, Cornelissen JJLM, Castón JR. Nanotechnological Applications Based on Bacterial Encapsulins. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1467. [PMID: 34206092 PMCID: PMC8229669 DOI: 10.3390/nano11061467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023]
Abstract
Encapsulins are proteinaceous nanocontainers, constructed by a single species of shell protein that self-assemble into 20-40 nm icosahedral particles. Encapsulins are structurally similar to the capsids of viruses of the HK97-like lineage, to which they are evolutionarily related. Nearly all these nanocontainers encase a single oligomeric protein that defines the physiological role of the complex, although a few encapsulate several activities within a single particle. Encapsulins are abundant in bacteria and archaea, in which they participate in regulation of oxidative stress, detoxification, and homeostasis of key chemical elements. These nanocontainers are physically robust, contain numerous pores that permit metabolite flux through the shell, and are very tolerant of genetic manipulation. There are natural mechanisms for efficient functionalization of the outer and inner shell surfaces, and for the in vivo and in vitro internalization of heterologous proteins. These characteristics render encapsulin an excellent platform for the development of biotechnological applications. Here we provide an overview of current knowledge of encapsulin systems, summarize the remarkable toolbox developed by researchers in this field, and discuss recent advances in the biomedical and bioengineering applications of encapsulins.
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Affiliation(s)
- Javier M. Rodríguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
| | - Carolina Allende-Ballestero
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
| | - Jeroen J. L. M. Cornelissen
- Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands;
| | - José R. Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
- Nanobiotechnology Associated Unit CNB-CSIC-IMDEA, Campus Cantoblanco, 28049 Madrid, Spain
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24
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Cesle EE, Filimonenko A, Tars K, Kalnins G. Variety of size and form of GRM2 bacterial microcompartment particles. Protein Sci 2021; 30:1035-1043. [PMID: 33763934 PMCID: PMC8040866 DOI: 10.1002/pro.4069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022]
Abstract
Bacterial microcompartments (BMCs) are bacterial organelles involved in enzymatic processes, such as carbon fixation, choline, ethanolamine and propanediol degradation, and others. Formed of a semi-permeable protein shell and an enzymatic core, they can enhance enzyme performance and protect the cell from harmful intermediates. With the ability to encapsulate non-native enzymes, BMCs show high potential for applied use. For this goal, a detailed look into shell form variability is significant to predict shell adaptability. Here we present four novel 3D cryo-EM maps of recombinant Klebsiella pneumoniae GRM2 BMC shell particles with the resolution in range of 9 to 22 Å and nine novel 2D classes corresponding to discrete BMC shell forms. These structures reveal icosahedral, elongated, oblate, multi-layered and polyhedral traits of BMCs, indicating considerable variation in size and form as well as adaptability during shell formation processes.
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Affiliation(s)
- Eva Emilija Cesle
- Structural Biology, Biotechnology and Virusology LaboratoryLatvian Biomedical Research and Study CentreRigaLatvia
| | - Anatolij Filimonenko
- CEITEC‐Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Kaspars Tars
- Structural Biology, Biotechnology and Virusology LaboratoryLatvian Biomedical Research and Study CentreRigaLatvia
- Faculty of BiologyUniversity of LatviaRigaLatvia
| | - Gints Kalnins
- Structural Biology, Biotechnology and Virusology LaboratoryLatvian Biomedical Research and Study CentreRigaLatvia
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25
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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: 13] [Impact Index Per Article: 4.3] [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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26
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Balabanova L, Averianova L, Marchenok M, Son O, Tekutyeva L. Microbial and Genetic Resources for Cobalamin (Vitamin B12) Biosynthesis: From Ecosystems to Industrial Biotechnology. Int J Mol Sci 2021; 22:ijms22094522. [PMID: 33926061 PMCID: PMC8123684 DOI: 10.3390/ijms22094522] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
Many microbial producers of coenzyme B12 family cofactors together with their metabolically interdependent pathways are comprehensively studied and successfully used both in natural ecosystems dominated by auxotrophs, including bacteria and mammals, and in the safe industrial production of vitamin B12. Metabolic reconstruction for genomic and metagenomic data and functional genomics continue to mine the microbial and genetic resources for biosynthesis of the vital vitamin B12. Availability of metabolic engineering techniques and usage of affordable and renewable sources allowed improving bioprocess of vitamins, providing a positive impact on both economics and environment. The commercial production of vitamin B12 is mainly achieved through the use of the two major industrial strains, Propionobacterium shermanii and Pseudomonas denitrificans, that involves about 30 enzymatic steps in the biosynthesis of cobalamin and completely replaces chemical synthesis. However, there are still unresolved issues in cobalamin biosynthesis that need to be elucidated for future bioprocess improvements. In the present work, we review the current state of development and challenges for cobalamin (vitamin B12) biosynthesis, describing the major and novel prospective strains, and the studies of environmental factors and genetic tools effecting on the fermentation process are reported.
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Affiliation(s)
- Larissa Balabanova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
- Correspondence:
| | - Liudmila Averianova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Maksim Marchenok
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Oksana Son
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Liudmila Tekutyeva
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
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27
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Liu LN. Bacterial metabolosomes: new insights into their structure and bioengineering. Microb Biotechnol 2021; 14:88-93. [PMID: 33404191 PMCID: PMC7888463 DOI: 10.1111/1751-7915.13740] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 12/18/2022] Open
Abstract
Bacterial metabolosomes have been discovered for over 25 years. They play essential roles in bacterial metabolism and pathogenesis. In this crystal ball paper, I will discuss the recent advances in the fundamental understanding and synthetic engineering of bacterial metabolosomes.
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Affiliation(s)
- Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.,College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
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28
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Kennedy NW, Ikonomova SP, Slininger Lee M, Raeder HW, Tullman-Ercek D. Self-assembling Shell Proteins PduA and PduJ have Essential and Redundant Roles in Bacterial Microcompartment Assembly. J Mol Biol 2020; 433:166721. [PMID: 33227310 DOI: 10.1016/j.jmb.2020.11.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 01/21/2023]
Abstract
Protein self-assembly is a common and essential biological phenomenon, and bacterial microcompartments present a promising model system to study this process. Bacterial microcompartments are large, protein-based organelles which natively carry out processes important for carbon fixation in cyanobacteria and the survival of enteric bacteria. These structures are increasingly popular with biological engineers due to their potential utility as nanobioreactors or drug delivery vehicles. However, the limited understanding of the assembly mechanism of these bacterial microcompartments hinders efforts to repurpose them for non-native functions. Here, we comprehensively investigate proteins involved in the assembly of the 1,2-propanediol utilization bacterial microcompartment from Salmonella enterica serovar Typhimurium LT2, one of the most widely studied microcompartment systems. We first demonstrate that two shell proteins, PduA and PduJ, have a high propensity for self-assembly upon overexpression, and we provide a novel method for self-assembly quantification. Using genomic knock-outs and knock-ins, we systematically show that these two proteins play an essential and redundant role in bacterial microcompartment assembly that cannot be compensated by other shell proteins. At least one of the two proteins PduA and PduJ must be present for the bacterial microcompartment shell to assemble. We also demonstrate that assembly-deficient variants of these proteins are unable to rescue microcompartment formation, highlighting the importance of this assembly property. Our work provides insight into the assembly mechanism of these bacterial organelles and will aid downstream engineering efforts.
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Affiliation(s)
- Nolan W Kennedy
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, United States
| | - Svetlana P Ikonomova
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - Marilyn Slininger Lee
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States; US Army Combat Capabilities Development Command Chemical Biological Center, Edgewood, MD, United States
| | - Henry W Raeder
- Molecular Biosciences Program, Weinberg College of Arts and Sciences, Northwestern University, Evanston, IL, United States
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States; Center for Synthetic Biology, Northwestern University, Evanston, IL, United States.
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29
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Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production. Nat Commun 2020; 11:5448. [PMID: 33116131 PMCID: PMC7595155 DOI: 10.1038/s41467-020-19280-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 10/07/2020] [Indexed: 11/30/2022] Open
Abstract
Compartmentalization is a ubiquitous building principle in cells, which permits segregation of biological elements and reactions. The carboxysome is a specialized bacterial organelle that encapsulates enzymes into a virus-like protein shell and plays essential roles in photosynthetic carbon fixation. The naturally designed architecture, semi-permeability, and catalytic improvement of carboxysomes have inspired rational design and engineering of new nanomaterials to incorporate desired enzymes into the protein shell for enhanced catalytic performance. Here, we build large, intact carboxysome shells (over 90 nm in diameter) in the industrial microorganism Escherichia coli by expressing a set of carboxysome protein-encoding genes. We develop strategies for enzyme activation, shell self-assembly, and cargo encapsulation to construct a robust nanoreactor that incorporates catalytically active [FeFe]-hydrogenases and functional partners within the empty shell for the production of hydrogen. We show that shell encapsulation and the internal microenvironment of the new catalyst facilitate hydrogen production of the encapsulated oxygen-sensitive hydrogenases. The study provides insights into the assembly and formation of carboxysomes and paves the way for engineering carboxysome shell-based nanoreactors to recruit specific enzymes for diverse catalytic reactions. The extreme oxygen sensitive character of hydrogenases is a longstanding issue for hydrogen production in bacteria. Here, the authors build carboxysome shells in E. coli and incorporate catalytically active hydrogenases and functional partners within the empty shell for the production of hydrogen.
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30
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Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein. Sci Rep 2020; 10:17501. [PMID: 33060756 PMCID: PMC7562746 DOI: 10.1038/s41598-020-74536-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/29/2020] [Indexed: 12/31/2022] Open
Abstract
Bacterial microcompartments (BMCs) are nanoscale proteinaceous organelles that encapsulate enzymes from the cytoplasm using an icosahedral protein shell that resembles viral capsids. Of particular interest are the carboxysomes (CBs), which sequester the CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to enhance carbon assimilation. The carboxysome shell serves as a semi-permeable barrier for passage of metabolites in and out of the carboxysome to enhance CO2 fixation. How the protein shell directs influx and efflux of molecules in an effective manner has remained elusive. Here we use molecular dynamics and umbrella sampling calculations to determine the free-energy profiles of the metabolic substrates, bicarbonate, CO2 and ribulose bisphosphate and the product 3-phosphoglycerate associated with their transition through the major carboxysome shell protein CcmK2. We elucidate the electrostatic charge-based permeability and key amino acid residues of CcmK2 functioning in mediating molecular transit through the central pore. Conformational changes of the loops forming the central pore may also be required for transit of specific metabolites. The importance of these in-silico findings is validated experimentally by site-directed mutagenesis of the key CcmK2 residue Serine 39. This study provides insight into the mechanism that mediates molecular transport through the shells of carboxysomes, applicable to other BMCs. It also offers a predictive approach to investigate and manipulate the shell permeability, with the intent of engineering BMC-based metabolic modules for new functions in synthetic biology.
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31
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Jones JA, Giessen TW. Advances in encapsulin nanocompartment biology and engineering. Biotechnol Bioeng 2020; 118:491-505. [PMID: 32918485 DOI: 10.1002/bit.27564] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/12/2020] [Accepted: 09/09/2020] [Indexed: 12/23/2022]
Abstract
Compartmentalization is an essential feature of all cells. It allows cells to segregate and coordinate physiological functions in a controlled and ordered manner. Different mechanisms of compartmentalization exist, with the most relevant to prokaryotes being encapsulation via self-assembling protein-based compartments. One widespread example of such is that of encapsulins-cage-like protein nanocompartments able to compartmentalize specific reactions, pathways, and processes in bacteria and archaea. While still relatively nascent bioengineering tools, encapsulins exhibit many promising characteristics, including a number of defined compartment sizes ranging from 24 to 42 nm, straightforward expression, the ability to self-assemble via the Hong Kong 97-like fold, marked physical robustness, and internal and external handles primed for rational genetic and molecular manipulation. Moreover, encapsulins allow for facile and specific encapsulation of native or heterologous cargo proteins via naturally or rationally fused targeting peptide sequences. Taken together, the attributes of encapsulins promise substantial customizability and broad usability. This review discusses recent advances in employing engineered encapsulins across various fields, from their use as bionanoreactors to targeted delivery systems and beyond. A special focus will be provided on the rational engineering of encapsulin systems and their potential promise as biomolecular research tools.
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Affiliation(s)
- Jesse A Jones
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Tobias W Giessen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
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32
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Stewart KL, Stewart AM, Bobik TA. Prokaryotic Organelles: Bacterial Microcompartments in E. coli and Salmonella. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0025-2019. [PMID: 33030141 PMCID: PMC7552817 DOI: 10.1128/ecosalplus.esp-0025-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Indexed: 02/07/2023]
Abstract
Bacterial microcompartments (MCPs) are proteinaceous organelles consisting of a metabolic pathway encapsulated within a selectively permeable protein shell. Hundreds of species of bacteria produce MCPs of at least nine different types, and MCP metabolism is associated with enteric pathogenesis, cancer, and heart disease. This review focuses chiefly on the four types of catabolic MCPs (metabolosomes) found in Escherichia coli and Salmonella: the propanediol utilization (pdu), ethanolamine utilization (eut), choline utilization (cut), and glycyl radical propanediol (grp) MCPs. Although the great majority of work done on catabolic MCPs has been carried out with Salmonella and E. coli, research outside the group is mentioned where necessary for a comprehensive understanding. Salient characteristics found across MCPs are discussed, including enzymatic reactions and shell composition, with particular attention paid to key differences between classes of MCPs. We also highlight relevant research on the dynamic processes of MCP assembly, protein targeting, and the mechanisms that underlie selective permeability. Lastly, we discuss emerging biotechnology applications based on MCP principles and point out challenges, unanswered questions, and future directions.
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Affiliation(s)
- Katie L. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Andrew M. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Thomas A. Bobik
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
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33
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Rubisco accumulation factor 1 (Raf1) plays essential roles in mediating Rubisco assembly and carboxysome biogenesis. Proc Natl Acad Sci U S A 2020; 117:17418-17428. [PMID: 32636267 PMCID: PMC7382273 DOI: 10.1073/pnas.2007990117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Carboxysomes are membrane-free organelles for carbon assimilation in cyanobacteria. The carboxysome consists of a proteinaceous shell that structurally resembles virus capsids and internal enzymes including ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), the primary carbon-fixing enzyme in photosynthesis. The formation of carboxysomes requires hierarchical self-assembly of thousands of protein subunits, initiated from Rubisco assembly and packaging to shell encapsulation. Here we study the role of Rubisco assembly factor 1 (Raf1) in Rubisco assembly and carboxysome formation in a model cyanobacterium, Synechococcus elongatus PCC7942 (Syn7942). Cryo-electron microscopy reveals that Raf1 facilitates Rubisco assembly by mediating RbcL dimer formation and dimer-dimer interactions. Syn7942 cells lacking Raf1 are unable to form canonical intact carboxysomes but generate a large number of intermediate assemblies comprising Rubisco, CcaA, CcmM, and CcmN without shell encapsulation and a low abundance of carboxysome-like structures with reduced dimensions and irregular shell shapes and internal organization. As a consequence, the Raf1-depleted cells exhibit reduced Rubisco content, CO2-fixing activity, and cell growth. Our results provide mechanistic insight into the chaperone-assisted Rubisco assembly and biogenesis of carboxysomes. Advanced understanding of the biogenesis and stepwise formation process of the biogeochemically important organelle may inform strategies for heterologous engineering of functional CO2-fixing modules to improve photosynthesis.
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