1
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Sheng Y, Chen Z, Cherrier MV, Martin L, Bui TTT, Li W, Lynham S, Nicolet Y, Ebrahimi KH. A Versatile Virus-Mimetic Engineering Approach for Concurrent Protein Nanocage Surface-Functionalization and Cargo Encapsulation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310913. [PMID: 38726952 DOI: 10.1002/smll.202310913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 04/26/2024] [Indexed: 08/02/2024]
Abstract
Naturally occurring protein nanocages like ferritin are self-assembled from multiple subunits. Because of their unique cage-like structure and biocompatibility, there is a growing interest in their biomedical use. A multipurpose and straightforward engineering approach does not exist for using nanocages to make drug-delivery systems by encapsulating hydrophilic or hydrophobic drugs and developing vaccines by surface functionalization with a protein like an antigen. Here, a versatile engineering approach is described by mimicking the HIV-1 Gap polyprotein precursor. Various PREcursors of nanoCages (PREC) are designed and created by linking two ferritin subunits via a flexible linker peptide containing a protease cleavage site. These precursors can have additional proteins at their N-terminus, and their protease cleavage generates ferritin-like nanocages named protease-induced nanocages (PINCs). It is demonstrated that PINC formation allows concurrent surface decoration with a protein and hydrophilic or hydrophobic drug encapsulation up to fourfold more than the amount achieved using other methods. The PINCs/Drug complex is stable and efficiently kills cancer cells. This work provides insight into the precursors' design rules and the mechanism of PINCs formation. The engineering approach and mechanistic insight described here will facilitate nanocages' applications in drug delivery or as a platform for making multifunctional therapeutics like mosaic vaccines.
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Affiliation(s)
- Yujie Sheng
- Faculty of Life Sciences and Medicine, Institute of Pharmaceutical Science, King's College London, London, SE1 9NH, UK
| | - Zilong Chen
- Faculty of Life Sciences and Medicine, Institute of Pharmaceutical Science, King's College London, London, SE1 9NH, UK
| | - Mickael V Cherrier
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, Grenoble, CS 10090, France
| | - Lydie Martin
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, Grenoble, CS 10090, France
| | - Tam T T Bui
- Randall Centre for Cell & Molecular Biophysics, King's College London, London, SE11UL, UK
| | - Wei Li
- Faculty of Life Sciences and Medicine, Institute of Pharmaceutical Science, King's College London, London, SE1 9NH, UK
| | - Steven Lynham
- Proteomics Core Facility, James Black Centre, King's College London, London, SE5 9NU, UK
| | - Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, Grenoble, CS 10090, France
| | - Kourosh H Ebrahimi
- Faculty of Life Sciences and Medicine, Institute of Pharmaceutical Science, King's College London, London, SE1 9NH, UK
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2
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Kumamoto S, Yamamoto A, Shiratsuchi Y, Matsuo K, Higashiura A, Hira D. Structural Investigations of Cargo Molecules Inside Icosahedrally Symmetric Encapsulin by VUVCD Spectroscopic Measurements. Chirality 2024; 36:e23700. [PMID: 39077830 DOI: 10.1002/chir.23700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/31/2024]
Abstract
Prokaryotes organize intracellular compartments with protein-based organelles called encapsulins. Encapsulins with icosahedral symmetry can encapsulate specific cargo proteins mediated by targeting peptides or encapsulation-mediating domains. Encapsulins have been used in eukaryotic cells for bioengineering, vaccine development, and nanoparticle alignment. Their versatility makes them attractive for research; however, detailed structural information on encapsulins is crucial for further applied research. However, cargo proteins are randomly oriented inside the icosahedral encapsulins. The random orientation of cargo proteins presents a challenge for structural analysis that relies on averaging processes such as x-ray crystallography and cryo-electron microscopy (cryo-EM) single-particle imaging. Therefore, we aimed to accurately estimate the secondary structure content and elucidate the structure of cargo proteins inside the particle by measuring the circular dichroism (CD) spectra using vacuum ultraviolet circular dichroism (VUVCD) spectroscopy. Thus, the structure of the cargo protein inside encapsulin was evaluated. This approach could potentially set a standard for evaluating cargo proteins inside particles in future applied research on encapsulins.
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Affiliation(s)
- Shiori Kumamoto
- Department of Biotechnology and Life Sciences, Sojo University, Kumamoto, Japan
| | - Akima Yamamoto
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yu Shiratsuchi
- Department of Materials Science and Engineering, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima, Japan
| | - Akifumi Higashiura
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Daisuke Hira
- Department of Biotechnology and Life Sciences, Sojo University, Kumamoto, Japan
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3
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Benisch R, Giessen TW. Structural and biochemical characterization of an encapsulin-associated rhodanese from Acinetobacter baumannii. Protein Sci 2024; 33:e5129. [PMID: 39073218 PMCID: PMC11284452 DOI: 10.1002/pro.5129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/07/2024] [Accepted: 07/14/2024] [Indexed: 07/30/2024]
Abstract
Rhodanese-like domains (RLDs) represent a widespread protein family canonically involved in sulfur transfer reactions between diverse donor and acceptor molecules. RLDs mediate these transsulfuration reactions via a transient persulfide intermediate, created by modifying a conserved cysteine residue in their active sites. RLDs are involved in various aspects of sulfur metabolism, including sulfide oxidation in mitochondria, iron-sulfur cluster biogenesis, and thio-cofactor biosynthesis. However, due to the inherent complexity of sulfur metabolism caused by the intrinsically high nucleophilicity and redox sensitivity of thiol-containing compounds, the physiological functions of many RLDs remain to be explored. Here, we focus on a single domain Acinetobacter baumannii RLD (Ab-RLD) associated with a desulfurase encapsulin which is able to store substantial amounts of sulfur inside its protein shell. We determine the 1.6 Å x-ray crystal structure of Ab-RLD, highlighting a homodimeric structure with a number of unusual features. We show through kinetic analysis that Ab-RLD exhibits thiosulfate sulfurtransferase activity with both cyanide and glutathione acceptors. Using native mass spectrometry and in vitro assays, we provide evidence that Ab-RLD can stably carry a persulfide and thiosulfate modification and may employ a ternary catalytic mechanism. Our results will inform future studies aimed at investigating the functional link between Ab-RLD and the desulfurase encapsulin.
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Affiliation(s)
- Robert Benisch
- Program in Chemical BiologyUniversity of MichiganAnn ArborMichiganUSA
| | - Tobias W. Giessen
- Program in Chemical BiologyUniversity of MichiganAnn ArborMichiganUSA
- Department of Biological ChemistryUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
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4
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Bhattacharya S, Jenkins MC, Keshavarz-Joud P, Bourque AR, White K, Alvarez Barkane AM, Bryksin AV, Hernandez C, Kopylov M, Finn M. Heterologous Prime-Boost with Immunologically Orthogonal Protein Nanoparticles for Peptide Immunofocusing. ACS NANO 2024; 18:20083-20100. [PMID: 39041587 PMCID: PMC11308774 DOI: 10.1021/acsnano.4c00949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/24/2024]
Abstract
Protein nanoparticles are effective platforms for antigen presentation and targeting effector immune cells in vaccine development. Encapsulins are a class of protein-based microbial nanocompartments that self-assemble into icosahedral structures with external diameters ranging from 24 to 42 nm. Encapsulins from Myxococcus xanthus were designed to package bacterial RNA when produced in E. coli and were shown to have immunogenic and self-adjuvanting properties enhanced by this RNA. We genetically incorporated a 20-mer peptide derived from a mutant strain of the SARS-CoV-2 receptor binding domain (RBD) into the encapsulin protomeric coat protein for presentation on the exterior surface of the particle, inducing the formation of several nonicosahedral structures that were characterized by cryogenic electron microscopy. This immunogen elicited conformationally relevant humoral responses to the SARS-CoV-2 RBD. Immunological recognition was enhanced when the same peptide was presented in a heterologous prime/boost vaccination strategy using the engineered encapsulin and a previously reported variant of the PP7 virus-like particle, leading to the development of a selective antibody response against a SARS-CoV-2 RBD point mutant. While generating epitope-focused antibody responses is an interplay between inherent vaccine properties and B/T cells, here we demonstrate the use of orthogonal nanoparticles to fine-tune the control of epitope focusing.
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Affiliation(s)
- Sonia Bhattacharya
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Matthew C. Jenkins
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Parisa Keshavarz-Joud
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Alisyn Retos Bourque
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Keiyana White
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Amina Maria Alvarez Barkane
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anton V. Bryksin
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Carolina Hernandez
- New
York Structural Biology Center, New York, New York 10027, United States
| | - Mykhailo Kopylov
- New
York Structural Biology Center, New York, New York 10027, United States
| | - M.G. Finn
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30332, United
States
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5
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Lučić M, Allport T, Clarke TA, Williams LJ, Wilson MT, Chaplin AK, Worrall JAR. The oligomeric states of dye-decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation. Protein Sci 2024; 33:e5073. [PMID: 38864770 PMCID: PMC11168072 DOI: 10.1002/pro.5073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/18/2024] [Accepted: 05/25/2024] [Indexed: 06/13/2024]
Abstract
A common evolutionary mechanism in biology to drive function is protein oligomerization. In prokaryotes, the symmetrical assembly of repeating protein units to form homomers is widespread, yet consideration in vitro of whether such assemblies have functional or mechanistic consequences is often overlooked. Dye-decolorizing peroxidases (DyPs) are one such example, where their dimeric α + β barrel units can form various oligomeric states, but the oligomer influence, if any, on mechanism and function has received little attention. In this work, we have explored the oligomeric state of three DyPs found in Streptomyces lividans, each with very different mechanistic behaviors in their reactions with hydrogen peroxide and organic substrates. Using analytical ultracentrifugation, we reveal that except for one of the A-type DyPs where only a single sedimenting species is detected, oligomer states ranging from homodimers to dodecamers are prevalent in solution. Using cryo-EM on preparations of the B-type DyP, we determined a 3.02 Å resolution structure of a hexamer assembly that corresponds to the dominant oligomeric state in solution as determined by analytical ultracentrifugation. Furthermore, cryo-EM data detected sub-populations of higher-order oligomers, with one of these formed by an arrangement of two B-type DyP hexamers to give a dodecamer assembly. Our solution and structural insights of these oligomer states provide a new framework to consider previous mechanistic studies of these DyP members and are discussed in terms of long-range electron transfer for substrate oxidation and in the "storage" of oxidizable equivalents on the heme until a two-electron donor is available.
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Affiliation(s)
- Marina Lučić
- School of Life SciencesUniversity of EssexColchesterUK
| | - Thomas Allport
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUK
| | | | | | | | - Amanda K. Chaplin
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUK
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6
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Van de Steen A, Wilkinson HC, Dalby PA, Frank S. Encapsulation of Transketolase into In Vitro-Assembled Protein Nanocompartments Improves Thermal Stability. ACS APPLIED BIO MATERIALS 2024; 7:3660-3674. [PMID: 38835217 PMCID: PMC11190991 DOI: 10.1021/acsabm.3c01153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/06/2024]
Abstract
Protein compartments offer definitive structures with a large potential design space that are of particular interest for green chemistry and therapeutic applications. One family of protein compartments, encapsulins, are simple prokaryotic nanocompartments that self-assemble from a single monomer into selectively permeable cages of between 18 and 42 nm. Over the past decade, encapsulins have been developed for a diverse application portfolio utilizing their defined cargo loading mechanisms and repetitive surface display. Although it has been demonstrated that encapsulation of non-native cargo proteins provides protection from protease activity, the thermal effects arising from enclosing cargo within encapsulins remain poorly understood. This study aimed to establish a methodology for loading a reporter protein into thermostable encapsulins to determine the resulting stability change of the cargo. Building on previous in vitro reassembly studies, we first investigated the effectiveness of in vitro reassembly and cargo-loading of two size classes of encapsulins Thermotoga maritima T = 1 and Myxococcus xanthus T = 3, using superfolder Green Fluorescent Protein. We show that the empty T. maritima capsid reassembles with higher yield than the M. xanthus capsid and that in vitro loading promotes the formation of the M. xanthus T = 3 capsid form over the T = 1 form, while overloading with cargo results in malformed T. maritima T = 1 encapsulins. For the stability study, a Förster resonance energy transfer (FRET)-probed industrially relevant enzyme cargo, transketolase, was then loaded into the T. maritima encapsulin. Our results show that site-specific orthogonal FRET labels can reveal changes in thermal unfolding of encapsulated cargo, suggesting that in vitro loading of transketolase into the T. maritima T = 1 encapsulin shell increases the thermal stability of the enzyme. This work supports the move toward fully harnessing structural, spatial, and functional control of in vitro assembled encapsulins with applications in cargo stabilization.
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Affiliation(s)
| | | | - Paul A. Dalby
- Department of Biochemical
Engineering, University College London, Bernard Katz Building, Gower Street, London WC1E 6BT, U.K.
| | - Stefanie Frank
- Department of Biochemical
Engineering, University College London, Bernard Katz Building, Gower Street, London WC1E 6BT, U.K.
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7
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Pandey KK, Sahoo BR, Pattnaik AK. Protein Nanoparticles as Vaccine Platforms for Human and Zoonotic Viruses. Viruses 2024; 16:936. [PMID: 38932228 PMCID: PMC11209504 DOI: 10.3390/v16060936] [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: 05/07/2024] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Vaccines are one of the most effective medical interventions, playing a pivotal role in treating infectious diseases. Although traditional vaccines comprise killed, inactivated, or live-attenuated pathogens that have resulted in protective immune responses, the negative consequences of their administration have been well appreciated. Modern vaccines have evolved to contain purified antigenic subunits, epitopes, or antigen-encoding mRNAs, rendering them relatively safe. However, reduced humoral and cellular responses pose major challenges to these subunit vaccines. Protein nanoparticle (PNP)-based vaccines have garnered substantial interest in recent years for their ability to present a repetitive array of antigens for improving immunogenicity and enhancing protective responses. Discovery and characterisation of naturally occurring PNPs from various living organisms such as bacteria, archaea, viruses, insects, and eukaryotes, as well as computationally designed structures and approaches to link antigens to the PNPs, have paved the way for unprecedented advances in the field of vaccine technology. In this review, we focus on some of the widely used naturally occurring and optimally designed PNPs for their suitability as promising vaccine platforms for displaying native-like antigens from human viral pathogens for protective immune responses. Such platforms hold great promise in combating emerging and re-emerging infectious viral diseases and enhancing vaccine efficacy and safety.
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Affiliation(s)
- Kush K. Pandey
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (K.K.P.); (B.R.S.)
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Bikash R. Sahoo
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (K.K.P.); (B.R.S.)
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Asit K. Pattnaik
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (K.K.P.); (B.R.S.)
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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8
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Eren E, Watts NR, Montecinos F, Wingfield PT. Encapsulated Ferritin-like Proteins: A Structural Perspective. Biomolecules 2024; 14:624. [PMID: 38927029 PMCID: PMC11202242 DOI: 10.3390/biom14060624] [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: 04/29/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Encapsulins are self-assembling nano-compartments that naturally occur in bacteria and archaea. These nano-compartments encapsulate cargo proteins that bind to the shell's interior through specific recognition sequences and perform various metabolic processes. Encapsulation enables organisms to perform chemical reactions without exposing the rest of the cell to potentially harmful substances while shielding cargo molecules from degradation and other adverse effects of the surrounding environment. One particular type of cargo protein, the ferritin-like protein (FLP), is the focus of this review. Encapsulated FLPs are members of the ferritin-like protein superfamily, and they play a crucial role in converting ferrous iron (Fe+2) to ferric iron (Fe+3), which is then stored inside the encapsulin in mineralized form. As such, FLPs regulate iron homeostasis and protect organisms against oxidative stress. Recent studies have demonstrated that FLPs have tremendous potential as biosensors and bioreactors because of their ability to catalyze the oxidation of ferrous iron with high specificity and efficiency. Moreover, they have been investigated as potential targets for therapeutic intervention in cancer drug development and bacterial pathogenesis. Further research will likely lead to new insights and applications for these remarkable proteins in biomedicine and biotechnology.
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Affiliation(s)
| | | | | | - Paul T. Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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9
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Eren E, Watts NR, Conway JF, Wingfield PT. Myxococcus xanthus encapsulin cargo protein EncD is a flavin-binding protein with ferric reductase activity. Proc Natl Acad Sci U S A 2024; 121:e2400426121. [PMID: 38748579 PMCID: PMC11126975 DOI: 10.1073/pnas.2400426121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/18/2024] [Indexed: 05/27/2024] Open
Abstract
Encapsulins are protein nanocompartments that regulate cellular metabolism in several bacteria and archaea. Myxococcus xanthus encapsulins protect the bacterial cells against oxidative stress by sequestering cytosolic iron. These encapsulins are formed by the shell protein EncA and three cargo proteins: EncB, EncC, and EncD. EncB and EncC form rotationally symmetric decamers with ferroxidase centers (FOCs) that oxidize Fe+2 to Fe+3 for iron storage in mineral form. However, the structure and function of the third cargo protein, EncD, have yet to be determined. Here, we report the x-ray crystal structure of EncD in complex with flavin mononucleotide. EncD forms an α-helical hairpin arranged as an antiparallel dimer, but unlike other flavin-binding proteins, it has no β-sheet, showing that EncD and its homologs represent a unique class of bacterial flavin-binding proteins. The cryo-EM structure of EncA-EncD encapsulins confirms that EncD binds to the interior of the EncA shell via its C-terminal targeting peptide. With only 100 amino acids, the EncD α-helical dimer forms the smallest flavin-binding domain observed to date. Unlike EncB and EncC, EncD lacks a FOC, and our biochemical results show that EncD instead is a NAD(P)H-dependent ferric reductase, indicating that the M. xanthus encapsulins act as an integrated system for iron homeostasis. Overall, this work contributes to our understanding of bacterial metabolism and could lead to the development of technologies for iron biomineralization and the production of iron-containing materials for the treatment of various diseases associated with oxidative stress.
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Affiliation(s)
- Elif Eren
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD20892
| | - Norman R. Watts
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD20892
| | - James F. Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15260
| | - Paul T. Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD20892
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10
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Szyszka TN, Andreas MP, Lie F, Miller LM, Adamson LSR, Fatehi F, Twarock R, Draper BE, Jarrold MF, Giessen TW, Lau YH. Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. Proc Natl Acad Sci U S A 2024; 121:e2321260121. [PMID: 38722807 PMCID: PMC11098114 DOI: 10.1073/pnas.2321260121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of unique symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryoelectron microscopy, we determine the structures of a precedented 60-mer icosahedral assembly and an unexpected 36-mer tetrahedron that features significant geometric rearrangements around a new interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple-point mutation to various amino acids and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent a unique example of tetrahedral geometry when surveying all characterized encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in the protein sequence.
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Affiliation(s)
- Taylor N. Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Felicia Lie
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
| | - Lohra M. Miller
- Chemistry Department, Indiana University, Bloomington, IN47405
| | | | - Farzad Fatehi
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
| | - Reidun Twarock
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
- Department of Biology, University of York, YorkYO10 5DD, United Kingdom
| | | | | | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
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11
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Andreas MP, Giessen TW. The biosynthesis of the odorant 2-methylisoborneol is compartmentalized inside a protein shell. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590730. [PMID: 38712110 PMCID: PMC11071394 DOI: 10.1101/2024.04.23.590730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Terpenoids are the largest class of natural products, found across all domains of life. One of the most abundant bacterial terpenoids is the volatile odorant 2-methylisoborneol (2-MIB), partially responsible for the earthy smell of soil and musty taste of contaminated water. Many bacterial 2-MIB biosynthetic gene clusters were thought to encode a conserved transcription factor, named EshA in the model soil bacterium Streptomyces griseus . Here, we revise the function of EshA, now referred to as Sg Enc, and show that it is a Family 2B encapsulin shell protein. Using cryo-electron microscopy, we find that Sg Enc forms an icosahedral protein shell and encapsulates 2-methylisoborneol synthase (2-MIBS) as a cargo protein. Sg Enc contains a cyclic adenosine monophosphate (cAMP) binding domain (CBD)-fold insertion and a unique metal-binding domain, both displayed on the shell exterior. We show that Sg Enc CBDs do not bind cAMP. We find that 2-MIBS cargo loading is mediated by an N-terminal disordered cargo-loading domain and that 2-MIBS activity and Sg Enc shell structure are not modulated by cAMP. Our work redefines the function of EshA and establishes Family 2B encapsulins as cargo-loaded protein nanocompartments involved in secondary metabolite biosynthesis.
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12
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Jones JA, Andreas MP, Giessen TW. Structural basis for peroxidase encapsulation inside the encapsulin from the Gram-negative pathogen Klebsiella pneumoniae. Nat Commun 2024; 15:2558. [PMID: 38519509 PMCID: PMC10960027 DOI: 10.1038/s41467-024-46880-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Encapsulins are self-assembling protein nanocompartments capable of selectively encapsulating dedicated cargo proteins, including enzymes involved in iron storage, sulfur metabolism, and stress resistance. They represent a unique compartmentalization strategy used by many pathogens to facilitate specialized metabolic capabilities. Encapsulation is mediated by specific cargo protein motifs known as targeting peptides (TPs), though the structural basis for encapsulation of the largest encapsulin cargo class, dye-decolorizing peroxidases (DyPs), is currently unknown. Here, we characterize a DyP-containing encapsulin from the enterobacterial pathogen Klebsiella pneumoniae. By combining cryo-electron microscopy with TP and TP-binding site mutagenesis, we elucidate the molecular basis for cargo encapsulation. TP binding is mediated by cooperative hydrophobic and ionic interactions as well as shape complementarity. Our results expand the molecular understanding of enzyme encapsulation inside protein nanocompartments and lay the foundation for rationally modulating encapsulin cargo loading for biomedical and biotechnological applications.
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Affiliation(s)
- Jesse A Jones
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
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13
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Williams TJ, Allen MA, Ray AE, Benaud N, Chelliah DS, Albanese D, Donati C, Selbmann L, Coleine C, Ferrari BC. Novel endolithic bacteria of phylum Chloroflexota reveal a myriad of potential survival strategies in the Antarctic desert. Appl Environ Microbiol 2024; 90:e0226423. [PMID: 38372512 PMCID: PMC10952385 DOI: 10.1128/aem.02264-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 02/20/2024] Open
Abstract
The ice-free McMurdo Dry Valleys of Antarctica are dominated by nutrient-poor mineral soil and rocky outcrops. The principal habitat for microorganisms is within rocks (endolithic). In this environment, microorganisms are provided with protection against sub-zero temperatures, rapid thermal fluctuations, extreme dryness, and ultraviolet and solar radiation. Endolithic communities include lichen, algae, fungi, and a diverse array of bacteria. Chloroflexota is among the most abundant bacterial phyla present in these communities. Among the Chloroflexota are four novel classes of bacteria, here named Candidatus Spiritibacteria class. nov. (=UBA5177), Candidatus Martimicrobia class. nov. (=UBA4733), Candidatus Tarhunnaeia class. nov. (=UBA6077), and Candidatus Uliximicrobia class. nov. (=UBA2235). We retrieved 17 high-quality metagenome-assembled genomes (MAGs) that represent these four classes. Based on genome predictions, all these bacteria are inferred to be aerobic heterotrophs that encode enzymes for the catabolism of diverse sugars. These and other organic substrates are likely derived from lichen, algae, and fungi, as metabolites (including photosynthate), cell wall components, and extracellular matrix components. The majority of MAGs encode the capacity for trace gas oxidation using high-affinity uptake hydrogenases, which could provide energy and metabolic water required for survival and persistence. Furthermore, some MAGs encode the capacity to couple the energy generated from H2 and CO oxidation to support carbon fixation (atmospheric chemosynthesis). All encode mechanisms for the detoxification and efflux of heavy metals. Certain MAGs encode features that indicate possible interactions with other organisms, such as Tc-type toxin complexes, hemolysins, and macroglobulins.IMPORTANCEThe ice-free McMurdo Dry Valleys of Antarctica are the coldest and most hyperarid desert on Earth. It is, therefore, the closest analog to the surface of the planet Mars. Bacteria and other microorganisms survive by inhabiting airspaces within rocks (endolithic). We identify four novel classes of phylum Chloroflexota, and, based on interrogation of 17 metagenome-assembled genomes, we predict specific metabolic and physiological adaptations that facilitate the survival of these bacteria in this harsh environment-including oxidation of trace gases and the utilization of nutrients (including sugars) derived from lichen, algae, and fungi. We propose that such adaptations allow these endolithic bacteria to eke out an existence in this cold and extremely dry habitat.
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Affiliation(s)
- Timothy J. Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Michelle A. Allen
- School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Angelique E. Ray
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Devan S. Chelliah
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Davide Albanese
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Claudio Donati
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, Viterbo, Italy
- Mycological Section, Italian Antarctic National Museum (MNA), Genova, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, Viterbo, Italy
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
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14
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Benisch R, Giessen TW. Structural and biochemical characterization of an encapsulin-associated rhodanese from Acinetobacter baumannii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.19.581022. [PMID: 38464153 PMCID: PMC10925157 DOI: 10.1101/2024.02.19.581022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Rhodanese-like domains (RLDs) represent a widespread protein family canonically involved in sulfur transfer reactions between diverse donor and acceptor molecules. RLDs mediate these transsulfuration reactions via a transient persulfide intermediate, created by modifying a conserved cysteine residue in their active sites. RLDs are involved in various aspects of sulfur metabolism, including sulfide oxidation in mitochondria, iron-sulfur cluster biogenesis, and thio-cofactor biosynthesis. However, due to the inherent complexity of sulfur metabolism caused by the intrinsically high nucleophilicity and redox sensitivity of thiol-containing compounds, the physiological functions of many RLDs remain to be explored. Here, we focus on a single domain Acinetobacter baumannii RLD (Ab-RLD) associated with a desulfurase encapsulin which is able to store substantial amounts of sulfur inside its protein shell. We determine the 1.6 Å x-ray crystal structure of Ab-RLD, highlighting a homodimeric structure with a number of unusual features. We show through kinetic analysis that Ab-RLD exhibits thiosulfate sulfurtransferase activity with both cyanide and glutathione acceptors. Using native mass spectrometry and in vitro assays, we provide evidence that Ab-RLD can stably carry a persulfide and thiosulfate modification and may employ a ternary catalytic mechanism. Our results will inform future studies aimed at investigating the functional link between Ab-RLD and the desulfurase encapsulin.
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Affiliation(s)
- Robert Benisch
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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15
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Bhattacharya S, Jenkins MC, Keshavarz-Joud P, Bourque AR, White K, Alvarez Barkane AM, Bryksin AV, Hernandez C, Kopylov M, Finn MG. Heterologous Prime-Boost with Immunologically Orthogonal Protein Nanoparticles for Peptide Immunofocusing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581861. [PMID: 38464232 PMCID: PMC10925081 DOI: 10.1101/2024.02.24.581861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Protein nanoparticles are effective platforms for antigen presentation and targeting effector immune cells in vaccine development. Encapsulins are a class of protein-based microbial nanocompartments that self-assemble into icosahedral structures with external diameters ranging from 24 to 42 nm. Encapsulins from Mxyococcus xanthus were designed to package bacterial RNA when produced in E. coli and were shown to have immunogenic and self-adjuvanting properties enhanced by this RNA. We genetically incorporated a 20-mer peptide derived from a mutant strain of the SARS-CoV-2 receptor binding domain (RBD) into the encapsulin protomeric coat protein for presentation on the exterior surface of the particle. This immunogen elicited conformationally-relevant humoral responses to the SARS-CoV-2 RBD. Immunological recognition was enhanced when the same peptide was presented in a heterologous prime/boost vaccination strategy using the engineered encapsulin and a previously reported variant of the PP7 virus-like particle, leading to the development of a selective antibody response against a SARS-CoV-2 RBD point mutant. While generating epitope-focused antibody responses is an interplay between inherent vaccine properties and B/T cells, here we demonstrate the use of orthogonal nanoparticles to fine-tune the control of epitope focusing.
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Affiliation(s)
- Sonia Bhattacharya
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Matthew C Jenkins
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Parisa Keshavarz-Joud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alisyn Retos Bourque
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Keiyana White
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Amina M Alvarez Barkane
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anton V Bryksin
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | | | - Mykhailo Kopylov
- New York Structural Biology Center, New York, New York, 10027, USA
| | - M G Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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16
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Benisch R, Andreas MP, Giessen TW. A widespread bacterial protein compartment sequesters and stores elemental sulfur. SCIENCE ADVANCES 2024; 10:eadk9345. [PMID: 38306423 PMCID: PMC10836720 DOI: 10.1126/sciadv.adk9345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Subcellular compartments often serve to store nutrients or sequester labile or toxic compounds. As bacteria mostly do not possess membrane-bound organelles, they often have to rely on protein-based compartments. Encapsulins are one of the most prevalent protein-based compartmentalization strategies found in prokaryotes. Here, we show that desulfurase encapsulins can sequester and store large amounts of crystalline elemental sulfur. We determine the 1.78-angstrom cryo-EM structure of a 24-nanometer desulfurase-loaded encapsulin. Elemental sulfur crystals can be formed inside the encapsulin shell in a desulfurase-dependent manner with l-cysteine as the sulfur donor. Sulfur accumulation can be influenced by the concentration and type of sulfur source in growth medium. The selectively permeable protein shell allows the storage of redox-labile elemental sulfur by excluding cellular reducing agents, while encapsulation substantially improves desulfurase activity and stability. These findings represent an example of a protein compartment able to accumulate and store elemental sulfur.
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Affiliation(s)
- Robert Benisch
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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17
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Fang Z, Zhu YJ, Qian ZG, Xia XX. Designer protein compartments for microbial metabolic engineering. Curr Opin Biotechnol 2024; 85:103062. [PMID: 38199036 DOI: 10.1016/j.copbio.2023.103062] [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: 10/02/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Protein compartments are distinct structures assembled in living cells via self-assembly or phase separation of specific proteins. Significant efforts have been made to discover their molecular structures and formation mechanisms, as well as their fundamental roles in spatiotemporal control of cellular metabolism. Here, we review the design and construction of synthetic protein compartments for spatial organization of target metabolic pathways toward increased efficiency and specificity. In particular, we highlight the compartmentalization strategies and recent examples to speed up desirable metabolic reactions, to reduce the accumulation of toxic metabolic intermediates, and to switch competing metabolic pathways. We also identify the most important challenges that need to be addressed for exploitation of these designer compartments as a versatile toolkit in metabolic reprogramming.
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Affiliation(s)
- Zhen Fang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Ya-Jiao Zhu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Zhi-Gang Qian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China.
| | - Xiao-Xia Xia
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China.
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18
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Chen Z, Wu T, Yu S, Li M, Fan X, Huo YX. Self-assembly systems to troubleshoot metabolic engineering challenges. Trends Biotechnol 2024; 42:43-60. [PMID: 37451946 DOI: 10.1016/j.tibtech.2023.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.
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Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Min Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Xuanhe Fan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China.
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19
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Liu J, Ran X, Li J, Wang H, Xue G, Wang Y. Novel insights into carbon nanomaterials enhancing anammox for nitrogen removal: Effects and mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167146. [PMID: 37726079 DOI: 10.1016/j.scitotenv.2023.167146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/21/2023]
Abstract
Carbon nanomaterials (CNMs) possess the properties including large specific surface area, high porosity, and stable chemical structures, presenting significant application advantages in wastewater treatment. Indeed, CNMs are considered to be added to anammox systems to strengthen anammox function, especially to resolve the challenge of anammox technology, i.e., the slow growth rate of anammox bacteria, as well as its high environmental sensitivity. This paper systematically reviews the promotion effects and mechanisms of CNMs on the nitrogen removal performance of anammox system. Among the zero-, one-, and two-dimensional CNMs, two-dimensional CNMs have best promoting effect on the nitrogen removal performance of anammox system due to its excellent conductivity and abundant functional groups. Then, the promotion effects of CNMs on anammox process are summarized from the perspective of anammox activity and bacteria abundance. Furthermore, CNMs not only enhance the anammox process, but also stimulate the coupling of denitrification pathways with anammox, as well as the improvement of system operational stability (alleviating the inhibitions of low temperature and pH fluctuation), thus contributing to the promoted nitrogen removal performance. Essentially, CNMs are capable of facilitating microbial immobilization and electron transfer, which favor to improve the efficiency and stability of anammox process. Finally, this review highlights the gap in knowledge and future work, aiming to provide a deeper understanding of how CNMs can strengthen the anammox system and provide a novel perspective for the engineering of the anammox process.
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Affiliation(s)
- Jiawei Liu
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Xiaochuan Ran
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Jia Li
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China.
| | - Gang Xue
- Shanghai Institute of Pollution Control and Ecological Security, Donghua University, Shanghai 201620, China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
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20
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Kwon S, Andreas MP, Giessen TW. Structure and heterogeneity of a highly cargo-loaded encapsulin shell. J Struct Biol 2023; 215:108022. [PMID: 37657675 DOI: 10.1016/j.jsb.2023.108022] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
Encapsulins are self-assembling protein nanocompartments able to selectively encapsulate dedicated cargo enzymes. Encapsulins are widespread across bacterial and archaeal phyla and are involved in oxidative stress resistance, iron storage, and sulfur metabolism. Encapsulin shells exhibit icosahedral geometry and consist of 60, 180, or 240 identical protein subunits. Cargo encapsulation is mediated by the specific interaction of targeting peptides or domains, found in all cargo proteins, with the interior surface of the encapsulin shell during shell self-assembly. Here, we report the 2.53 Å cryo-EM structure of a heterologously produced and highly cargo-loaded T3 encapsulin shell from Myxococcus xanthus and explore the systems' structural heterogeneity. We find that exceedingly high cargo loading results in the formation of substantial amounts of distorted and aberrant shells, likely caused by a combination of unfavorable steric clashes of cargo proteins and shell conformational changes. Based on our cryo-EM structure, we determine and analyze the targeting peptide-shell binding mode. We find that both ionic and hydrophobic interactions mediate targeting peptide binding. Our results will guide future attempts at rationally engineering encapsulins for biomedical and biotechnological applications.
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Affiliation(s)
- Seokmu Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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21
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Fung HKH, Hayashi Y, Salo VT, Babenko A, Zagoriy I, Brunner A, Ellenberg J, Müller CW, Cuylen-Haering S, Mahamid J. Genetically encoded multimeric tags for subcellular protein localization in cryo-EM. Nat Methods 2023; 20:1900-1908. [PMID: 37932397 PMCID: PMC10703698 DOI: 10.1038/s41592-023-02053-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
Cryo-electron tomography (cryo-ET) allows for label-free high-resolution imaging of macromolecular assemblies in their native cellular context. However, the localization of macromolecules of interest in tomographic volumes can be challenging. Here we present a ligand-inducible labeling strategy for intracellular proteins based on fluorescent, 25-nm-sized, genetically encoded multimeric particles (GEMs). The particles exhibit recognizable structural signatures, enabling their automated detection in cryo-ET data by convolutional neural networks. The coupling of GEMs to green fluorescent protein-tagged macromolecules of interest is triggered by addition of a small-molecule ligand, allowing for time-controlled labeling to minimize disturbance to native protein function. We demonstrate the applicability of GEMs for subcellular-level localization of endogenous and overexpressed proteins across different organelles in human cells using cryo-correlative fluorescence and cryo-ET imaging. We describe means for quantifying labeling specificity and efficiency, and for systematic optimization for rare and abundant protein targets, with emphasis on assessing the potential effects of labeling on protein function.
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Affiliation(s)
- Herman K H Fung
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Yuki Hayashi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Veijo T Salo
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Anastasiia Babenko
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- University of Heidelberg, Heidelberg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Brunner
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Sara Cuylen-Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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22
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Kaltbeitzel J, Wich PR. Protein-based Nanoparticles: From Drug Delivery to Imaging, Nanocatalysis and Protein Therapy. Angew Chem Int Ed Engl 2023; 62:e202216097. [PMID: 36917017 DOI: 10.1002/anie.202216097] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/16/2023]
Abstract
Proteins and enzymes are versatile biomaterials for a wide range of medical applications due to their high specificity for receptors and substrates, high degradability, low toxicity, and overall good biocompatibility. Protein nanoparticles are formed by the arrangement of several native or modified proteins into nanometer-sized assemblies. In this review, we will focus on artificial nanoparticle systems, where proteins are the main structural element and not just an encapsulated payload. While under natural conditions, only certain proteins form defined aggregates and nanoparticles, chemical modifications or a change in the physical environment can further extend the pool of available building blocks. This allows the assembly of many globular proteins and even enzymes. These advances in preparation methods led to the emergence of new generations of nanosystems that extend beyond transport vehicles to diverse applications, from multifunctional drug delivery to imaging, nanocatalysis and protein therapy.
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Affiliation(s)
- Jonas Kaltbeitzel
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Peter R Wich
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia
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23
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Quinton AR, McDowell HB, Hoiczyk E. Encapsulins: Nanotechnology's future in a shell. ADVANCES IN APPLIED MICROBIOLOGY 2023; 125:1-48. [PMID: 38783722 DOI: 10.1016/bs.aambs.2023.09.001] [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: 05/25/2024]
Abstract
Encapsulins, virus capsid-like bacterial nanocompartments have emerged as promising tools in medicine, imaging, and material sciences. Recent work has shown that these protein-bound icosahedral 'organelles' possess distinct properties that make them exceptionally usable for nanotechnology applications. A key factor contributing to their appeal is their ability to self-assemble, coupled with their capacity to encapsulate a wide range of cargos. Their genetic manipulability, stability, biocompatibility, and nano-size further enhance their utility, offering outstanding possibilities for practical biotechnology applications. In particular, their amenability to engineering has led to their extensive modification, including the packaging of non-native cargos and the utilization of the shell surface for displaying immunogenic or targeting proteins and peptides. This inherent versatility, combined with the ease of expressing encapsulins in heterologous hosts, promises to provide broad usability. Although mostly not yet commercialized, encapsulins have started to demonstrate their vast potential for biotechnology, from drug delivery to biofuel production and the synthesis of valuable inorganic materials. In this review, we will initially discuss the structure, function and diversity of encapsulins, which form the basis for these emerging applications, before reviewing ongoing practical uses and highlighting promising applications in medicine, engineering and environmental sciences.
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Affiliation(s)
- Amy Ruth Quinton
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Harry Benjamin McDowell
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Egbert Hoiczyk
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom.
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24
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Su Y, Liu B, Huang Z, Teng Z, Yang L, Zhu J, Huo S, Liu A. Virus-like particles nanoreactors: from catalysis towards bio-applications. J Mater Chem B 2023; 11:9084-9098. [PMID: 37697810 DOI: 10.1039/d3tb01112g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Virus-like particles (VLPs) are self-assembled supramolecular structures found in nature, often used for compartmentalization. Exploiting their inherent properties, including precise nanoscale structures, monodispersity, and high stability, these architectures have been widely used as nanocarriers to protect or enrich catalysts, facilitating catalytic reactions and avoiding interference from the bulk solutions. In this review, we summarize the current progress of virus-like particles (VLPs)-based nanoreactors. First, we briefly introduce the physicochemical properties of the most commonly used virus particles to understand their roles in catalytic reactions beyond the confined space. Next, we summarize the self-assembly of nanoreactors forming higher-order hierarchical structures, highlighting the emerging field of nanoreactors as artificial organelles and their potential biomedical applications. Finally, we discuss the current findings and future perspectives of VLPs-based nanoreactors.
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Affiliation(s)
- Yuqing Su
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Beibei Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Zhenkun Huang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Zihao Teng
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Liulin Yang
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Jie Zhu
- National-Local Joint Engineering Research and High-Quality Utilization, Changzhou University, Changzhou 213164, China
| | - Shuaidong Huo
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Aijie Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
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25
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Williams SM, Chatterji D. Dps Functions as a Key Player in Bacterial Iron Homeostasis. ACS OMEGA 2023; 8:34299-34309. [PMID: 37779979 PMCID: PMC10536872 DOI: 10.1021/acsomega.3c03277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023]
Abstract
Iron plays a vital role in the maintenance of life, being central to various cellular processes, from respiration to gene regulation. It is essential for iron to be stored in a nontoxic and readily available form. DNA binding proteins under starvation (Dps) belong to the ferritin family of iron storage proteins and are adept at storing iron in their hollow protein shells. Existing solely in prokaryotes, these proteins have the additional functions of DNA binding and protection from oxidative stress. Iron storage proteins play a functional role in storage, release, and transfer of iron and therefore are central to the optimal functioning of iron homeostasis. Here we review the multifarious properties of Dps through relevant biochemical and structural studies with a focus on iron storage and ferroxidation. We also examine the role of Dps as a possible candidate as an iron donor to iron-sulfur (Fe-S) clusters, which are ubiquitous to many biological processes.
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Affiliation(s)
- Sunanda Margrett Williams
- Institute
of Structural and Molecular Biology, Birkbeck,
University of London, Malet Street, London WC1E
7HX, United Kingdom
| | - Dipankar Chatterji
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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26
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Jones JA, Andreas MP, Giessen TW. Structural basis for peroxidase encapsulation in a protein nanocompartment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558302. [PMID: 37790520 PMCID: PMC10542125 DOI: 10.1101/2023.09.18.558302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Encapsulins are self-assembling protein nanocompartments capable of selectively encapsulating dedicated cargo proteins, including enzymes involved in iron storage, sulfur metabolism, and stress resistance. They represent a unique compartmentalization strategy used by many pathogens to facilitate specialized metabolic capabilities. Encapsulation is mediated by specific cargo protein motifs known as targeting peptides (TPs), though the structural basis for encapsulation of the largest encapsulin cargo class, dye-decolorizing peroxidases (DyPs), is currently unknown. Here, we characterize a DyP-containing encapsulin from the enterobacterial pathogen Klebsiella pneumoniae. By combining cryo-electron microscopy with TP mutagenesis, we elucidate the molecular basis for cargo encapsulation. TP binding is mediated by cooperative hydrophobic and ionic interactions as well as shape complementarity. Our results expand the molecular understanding of enzyme encapsulation inside protein nanocompartments and lay the foundation for rationally modulating encapsulin cargo loading for biomedical and biotechnological applications.
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Affiliation(s)
- Jesse A. Jones
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
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27
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Kwon S, Andreas MP, Giessen TW. Structure and heterogeneity of a highly cargo-loaded encapsulin shell. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550694. [PMID: 37546724 PMCID: PMC10402063 DOI: 10.1101/2023.07.26.550694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Encapsulins are self-assembling protein nanocompartments able to selectively encapsulate dedicated cargo enzymes. Encapsulins are widespread across bacterial and archaeal phyla and are involved in oxidative stress resistance, iron storage, and sulfur metabolism. Encapsulin shells exhibit icosahedral geometry and consist of 60, 180, or 240 identical protein subunits. Cargo encapsulation is mediated by the specific interaction of targeting peptides or domains, found in all cargo proteins, with the interior surface of the encapsulin shell during shell self-assembly. Here, we report the 2.53 Å cryo-EM structure of a heterologously produced and highly cargo-loaded T3 encapsulin shell from Myxococcus xanthus and explore the systems' structural heterogeneity. We find that exceedingly high cargo loading results in the formation of substantial amounts of distorted and aberrant shells, likely caused by a combination of unfavorable steric clashes of cargo proteins and shell conformational changes. Based on our cryo-EM structure, we determine and analyze the targeting peptide-shell binding mode. We find that both ionic and hydrophobic interactions mediate targeting peptide binding. Our results will guide future attempts at rationally engineering encapsulins for biomedical and biotechnological applications.
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Affiliation(s)
- Seokmu Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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28
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Abstract
Encapsulins are a recently discovered class of prokaryotic self-assembling icosahedral protein nanocompartments measuring between 24 and 42 nm in diameter, capable of selectively encapsulating dedicated cargo proteins in vivo. They have been classified into four families based on sequence identity and operon structure, and thousands of encapsulin systems have recently been computationally identified across a wide range of bacterial and archaeal phyla. Cargo encapsulation is mediated by the presence of specific targeting motifs found in all native cargo proteins that interact with the interior surface of the encapsulin shell during self-assembly. Short C-terminal targeting peptides (TPs) are well documented in Family 1 encapsulins, while more recently, larger N-terminal targeting domains (TDs) have been discovered in Family 2. The modular nature of TPs and their facile genetic fusion to non-native cargo proteins of interest has made cargo encapsulation, both in vivo and in vitro, readily exploitable and has therefore resulted in a range of rationally engineered nano-compartmentalization systems. This review summarizes current knowledge on cargo protein encapsulation within encapsulins and highlights select studies that utilize TP fusions to non-native cargo in creative and useful ways.
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Affiliation(s)
- Jesse A Jones
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Robert Benisch
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
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29
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Babar TK, Glare TR, Hampton JG, Hurst MRH, Narciso J, Sheen CR, Koch B. Linocin M18 protein from the insect pathogenic bacterium Brevibacillus laterosporus isolates. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12563-8. [PMID: 37204448 DOI: 10.1007/s00253-023-12563-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/19/2023] [Accepted: 04/29/2023] [Indexed: 05/20/2023]
Abstract
Brevibacillus laterosporus (Bl) is a Gram-positive and spore-forming bacterium. Insect pathogenic strains have been characterised in New Zealand, and two isolates, Bl 1821L and Bl 1951, are under development for use in biopesticides. However, growth in culture is sometimes disrupted, affecting mass production. Based on previous work, it was hypothesised that Tectiviridae phages might be implicated. While investigating the cause of the disrupted growth, electron micrographs of crude lysates showed structural components of putative phages including capsid and tail-like structures. Sucrose density gradient purification yielded a putative self-killing protein of ~30 kDa. N-terminal sequencing of the ~30 kDa protein identified matches to a predicted 25 kDa hypothetical and a 31.4 kDa putative encapsulating protein homologs, with the genes encoding each protein adjacent in the genomes. BLASTp analysis of the homologs of 31.4 kDa amino acid sequences shared 98.6% amino acid identity to the Linocin M18 bacteriocin family protein of Brevibacterium sp. JNUCC-42. Bioinformatic tools including AMPA and CellPPD defined that the bactericidal potential originated from a putative encapsulating protein. Antagonistic activity of the ~30 kDa encapsulating protein of Bl 1821L and Bl 1951during growth in broth exhibited bacterial autolytic activity. LIVE/DEAD staining of Bl 1821L cells after treatment with the ~30 kDa encapsulating protein of Bl 1821L substantiated the findings by showing 58.8% cells with the compromised cell membranes as compared to 37.5% cells in the control. Furthermore, antibacterial activity of the identified proteins of Bl 1821L was validated through gene expression in a Gram-positive bacterium Bacillus subtilis WB800N. KEY POINTS: • Gene encoding the 31.4 kDa antibacterial Linocin M18 protein was identified • It defined the autocidal activity of Linocin M18 (encapsulating) protein • Identified the possible killing mechanism of the encapsulins.
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Affiliation(s)
- Tauseef K Babar
- Bio-Protection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand.
- Department of Entomology, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, 60000, Pakistan.
| | - Travis R Glare
- Bio-Protection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
| | - John G Hampton
- Bio-Protection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
| | - Mark R H Hurst
- Resilient Agriculture, AgResearch, Lincoln Research Centre, Christchurch, New Zealand
| | - Josefina Narciso
- Bio-Protection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
| | - Campbell R Sheen
- Protein Science and Engineering, Callaghan Innovation, Christchurch, New Zealand
| | - Barbara Koch
- Protein Science and Engineering, Callaghan Innovation, Christchurch, New Zealand
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30
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Abrahamson CH, Palmero BJ, Kennedy NW, Tullman-Ercek D. Theoretical and Practical Aspects of Multienzyme Organization and Encapsulation. Annu Rev Biophys 2023; 52:553-572. [PMID: 36854212 DOI: 10.1146/annurev-biophys-092222-020832] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The advent of biotechnology has enabled metabolic engineers to assemble heterologous pathways in cells to produce a variety of products of industrial relevance, often in a sustainable way. However, many pathways face challenges of low product yield. These pathways often suffer from issues that are difficult to optimize, such as low pathway flux and off-target pathway consumption of intermediates. These issues are exacerbated by the need to balance pathway flux with the health of the cell, particularly when a toxic intermediate builds up. Nature faces similar challenges and has evolved spatial organization strategies to increase metabolic pathway flux and efficiency. Inspired by these strategies, bioengineers have developed clever strategies to mimic spatial organization in nature. This review explores the use of spatial organization strategies, including protein scaffolding and protein encapsulation inside of proteinaceous shells, toward overcoming bottlenecks in metabolic engineering efforts.
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Affiliation(s)
- Charlotte H Abrahamson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA;
| | - Brett J Palmero
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois, USA
| | - Nolan W Kennedy
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA;
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
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31
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Hu L, Wang Y, Wang L, Xiao S, Zheng Y, Yin G, Du G, Chen J, Kang Z. Construction of Osmotic Pressure Responsive Vacuole-like Bacterial Organelles with Capsular Polysaccharides as Building Blocks. ACS Synth Biol 2023; 12:750-760. [PMID: 36872621 DOI: 10.1021/acssynbio.2c00546] [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: 03/07/2023]
Abstract
Many artificial organelles or subcellular compartments have been developed to tune gene expression, regulate metabolic pathways, or endow new cell functions. Most of these organelles or compartments were built using proteins or nucleic acids as building blocks. In this study, we demonstrated that capsular polysaccharide (CPS) retained inside bacteria cytosol assembled into mechanically stable CPS compartments. The CPS compartments were able to accommodate and release protein molecules but not lipids or nucleic acids. Intriguingly, we found that the CPS compartment size responds to osmotic stress and this compartment improves cell survival under high osmotic pressures, which was similar to the vacuole functionalities. By fine-tuning the synthesis and degradation of CPS with osmotic stress-responsive promoters, we achieved dynamic regulation of the size of CPS compartments and the host cells in response to external osmotic stress. Our results shed new light on developing prokaryotic artificial organelles with carbohydrate macromolecules.
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Affiliation(s)
- Litao Hu
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yang Wang
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Lingling Wang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Sen Xiao
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yilin Zheng
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guobin Yin
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhen Kang
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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32
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Jones JA, Andreas MP, Giessen TW. Exploring the Extreme Acid Tolerance of a Dynamic Protein Nanocage. Biomacromolecules 2023; 24:1388-1399. [PMID: 36796007 DOI: 10.1021/acs.biomac.2c01424] [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] [Indexed: 02/18/2023]
Abstract
Encapsulins are microbial protein nanocages capable of efficient self-assembly and cargo enzyme encapsulation. Due to their favorable properties, including high thermostability, protease resistance, and robust heterologous expression, encapsulins have become popular bioengineering tools for applications in medicine, catalysis, and nanotechnology. Resistance against physicochemical extremes like high temperature and low pH is a highly desirable feature for many biotechnological applications. However, no systematic search for acid-stable encapsulins has been carried out, while the influence of pH on encapsulin shells has so far not been thoroughly explored. Here, we report on a newly identified encapsulin nanocage from the acid-tolerant bacterium Acidipropionibacterium acidipropionici. Using transmission electron microscopy, dynamic light scattering, and proteolytic assays, we demonstrate its extreme acid tolerance and resilience against proteases. We structurally characterize the novel nanocage using cryo-electron microscopy, revealing a dynamic five-fold pore that displays distinct "closed" and "open" states at neutral pH but only a singular "closed" state under strongly acidic conditions. Further, the "open" state exhibits the largest pore in an encapsulin shell reported to date. Non-native protein encapsulation capabilities are demonstrated, and the influence of external pH on internalized cargo is explored. Our results expand the biotechnological application range of encapsulin nanocages toward potential uses under strongly acidic conditions and highlight pH-responsive encapsulin pore dynamics.
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Affiliation(s)
- Jesse A Jones
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0624, United States
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0624, United States
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0624, United States
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan 48109-1382, United States
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33
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Tailored Functionalized Protein Nanocarriers for Cancer Therapy: Recent Developments and Prospects. Pharmaceutics 2023; 15:pharmaceutics15010168. [PMID: 36678796 PMCID: PMC9861211 DOI: 10.3390/pharmaceutics15010168] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Recently, the potential use of nanoparticles for the targeted delivery of therapeutic and diagnostic agents has garnered increased interest. Several nanoparticle drug delivery systems have been developed for cancer treatment. Typically, protein-based nanocarriers offer several advantages, including biodegradability and biocompatibility. Using genetic engineering or chemical conjugation approaches, well-known naturally occurring protein nanoparticles can be further prepared, engineered, and functionalized in their self-assembly to meet the demands of clinical production efficiency. Accordingly, promising protein nanoparticles have been developed with outstanding tumor-targeting capabilities, ultimately overcoming multidrug resistance issues, in vivo delivery barriers, and mimicking the tumor microenvironment. Bioinspired by natural nanoparticles, advanced computational techniques have been harnessed for the programmable design of highly homogenous protein nanoparticles, which could open new routes for the rational design of vaccines and drug formulations. The current review aims to present several significant advancements made in protein nanoparticle technology, and their use in cancer therapy. Additionally, tailored construction methods and therapeutic applications of engineered protein-based nanoparticles are discussed.
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34
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Chmelyuk NS, Oda VV, Gabashvili AN, Abakumov MA. Encapsulins: Structure, Properties, and Biotechnological Applications. BIOCHEMISTRY (MOSCOW) 2023; 88:35-49. [PMID: 37068871 PMCID: PMC9937530 DOI: 10.1134/s0006297923010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
In 1994 a new class of prokaryotic compartments was discovered, collectively called "encapsulins" or "nanocompartments". Encapsulin shell protomer proteins self-assemble to form icosahedral structures of various diameters (24-42 nm). Inside of nanocompartments shells, one or several cargo proteins, diverse in their functions, can be encapsulated. In addition, non-native cargo proteins can be loaded into nanocompartments, and shell surfaces can be modified via various compounds, which makes it possible to create targeted drug delivery systems, labels for optical and MRI imaging, and to use encapsulins as bioreactors. This review describes a number of strategies of encapsulins application in various fields of science, including biomedicine and nanobiotechnologies.
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Affiliation(s)
- Nelly S Chmelyuk
- National University of Science and Technology "MISIS", Moscow, 119049, Russia
- Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, Moscow, 117977, Russia
| | - Vera V Oda
- National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | - Anna N Gabashvili
- National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | - Maxim A Abakumov
- National University of Science and Technology "MISIS", Moscow, 119049, Russia.
- Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, Moscow, 117977, Russia
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35
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Timmermans SBPE, Mesman R, Blezer KJR, van Niftrik L, van Hest JCM. Cargo-loading of hybrid cowpea chlorotic mottle virus capsids via a co-expression approach. Virology 2022; 577:99-104. [PMID: 36335770 DOI: 10.1016/j.virol.2022.10.011] [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: 07/19/2022] [Revised: 10/12/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Capsids of the cowpea chlorotic mottle virus (CCMV) are great candidates for the development into in vivo catalytic or therapeutic nanocarriers. However, due to their limited intrinsic stability at physiological pH, thus far no methods exist for incorporating cargo into these nanoparticles in cellulo. Here, we employ a stabilized VW1-VW8 ELP-CCMV variant for the development of a co-expression-based cargo-loading approach. Co-expression of the non-functionalized VW1-VW8 ELP-CCMV coat protein with fusion proteins with enhanced green fluorescent protein (mEGFP) and pyrrolysine synthase D (PylD) in E. coli enabled the purification of cargo-loaded capsids from the bacteria directly either via affinity chromatography or PEG-precipitation and subsequent size exclusion chromatography. Microscopy results indicated that the co-expression does not harm the E. coli cells and that proper folding of the mEGFP domain is not hampered by the co-assembly. Our co-expression strategy is thus a suitable approach to produce cargo-loaded CCMV nanoparticles.
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Affiliation(s)
- Suzanne B P E Timmermans
- Bio-Organic Chemistry Research Group Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513 (STO3.41), 5600, MB, Eindhoven, the Netherlands
| | - Rob Mesman
- Microbial Cell Biology & Biochemistry Research Group, Department of Microbiology, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands
| | - Kim J R Blezer
- Bio-Organic Chemistry Research Group Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513 (STO3.41), 5600, MB, Eindhoven, the Netherlands
| | - Laura van Niftrik
- Microbial Cell Biology & Biochemistry Research Group, Department of Microbiology, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands
| | - Jan C M van Hest
- Bio-Organic Chemistry Research Group Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513 (STO3.41), 5600, MB, Eindhoven, the Netherlands.
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36
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Kwon S, Giessen TW. Engineered Protein Nanocages for Concurrent RNA and Protein Packaging In Vivo. ACS Synth Biol 2022; 11:3504-3515. [PMID: 36170610 PMCID: PMC9944510 DOI: 10.1021/acssynbio.2c00391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Protein nanocages have emerged as an important engineering platform for biotechnological and biomedical applications. Among naturally occurring protein cages, encapsulin nanocompartments have recently gained prominence due to their favorable physico-chemical properties, ease of shell modification, and highly efficient and selective intrinsic protein packaging capabilities. Here, we expand encapsulin function by designing and characterizing encapsulins for concurrent RNA and protein encapsulation in vivo. Our strategy is based on modifying encapsulin shells with nucleic acid-binding peptides without disrupting the native protein packaging mechanism. We show that our engineered encapsulins reliably self-assemble in vivo, are capable of efficient size-selective in vivo RNA packaging, can simultaneously load multiple functional RNAs, and can be used for concurrent in vivo packaging of RNA and protein. Our engineered encapsulation platform has potential for codelivery of therapeutic RNAs and proteins to elicit synergistic effects and as a modular tool for other biotechnological applications.
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Affiliation(s)
- Seokmu Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tobias W. Giessen
- Department of Biological Chemistry and Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
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37
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Cappelli L, Cinelli P, Giusti F, Ferlenghi I, Utrio-Lanfaloni S, Wahome N, Bottomley MJ, Maione D, Cozzi R. Self-assembling protein nanoparticles and virus like particles correctly display β-barrel from meningococcal factor H-binding protein through genetic fusion. PLoS One 2022; 17:e0273322. [PMID: 36112575 PMCID: PMC9480994 DOI: 10.1371/journal.pone.0273322] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/06/2022] [Indexed: 12/04/2022] Open
Abstract
Recombinant protein-based vaccines are a valid and safer alternative to traditional vaccines based on live-attenuated or killed pathogens. However, the immune response of subunit vaccines is generally lower compared to that elicited by traditional vaccines and usually requires the use of adjuvants. The use of self-assembling protein nanoparticles, as a platform for vaccine antigen presentation, is emerging as a promising approach to enhance the production of protective and functional antibodies. In this work we demonstrated the successful repetitive antigen display of the C-terminal β-barrel domain of factor H binding protein, derived from serogroup B Meningococcus on the surface of different self-assembling nanoparticles using genetic fusion. Six nanoparticle scaffolds were tested, including virus-like particles with different sizes, geometries, and physicochemical properties. Combining computational and structure-based rational design we were able generate antigen-fused scaffolds that closely aligned with three-dimensional structure predictions. The chimeric nanoparticles were produced as recombinant proteins in Escherichia coli and evaluated for solubility, stability, self-assembly, and antigen accessibility using a variety of biophysical methods. Several scaffolds were identified as being suitable for genetic fusion with the β-barrel from fHbp, including ferritin, a de novo designed aldolase from Thermotoga maritima, encapsulin, CP3 phage coat protein, and the Hepatitis B core antigen. In conclusion, a systematic screening of self-assembling nanoparticles has been applied for the repetitive surface display of a vaccine antigen. This work demonstrates the capacity of rational structure-based design to develop new chimeric nanoparticles and describes a strategy that can be utilized to discover new nanoparticle-based approaches in the search for vaccines against bacterial pathogens.
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Affiliation(s)
| | - Paolo Cinelli
- University of Bologna, Bologna, Italy
- GSK, Siena, Italy
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38
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Zhang Q, Lin JG, Kong Z, Zhang Y. A critical review of exogenous additives for improving the anammox process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155074. [PMID: 35398420 DOI: 10.1016/j.scitotenv.2022.155074] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/22/2022] [Accepted: 04/02/2022] [Indexed: 06/14/2023]
Abstract
Anammox achieves chemoautotrophic nitrogen removal under anaerobic and anoxic conditions and is a low-carbon wastewater biological nitrogen removal process with broad application potential. However, the physiological limitations of AnAOB often cause problems in engineering applications, such as a long start-up time, unstable operation, easily inhibited reactions, and difficulty in long-term strain preservation. Exogenous additives have been considered an alternative strategy to address these issues by retaining microbes, shortening the doubling time of AnAOB and improving functional enzyme activity. This paper reviews the role of carriers, biochar, intermediates, metal ions, reaction substrates, redox buffers, cryoprotectants and organics in optimizing anammox. The pathways and mechanisms of exogenous additives, which are explored to solve problems, are systematically summarized and analyzed in this article according to operational performance, functional enzyme activity, and microbial abundance to provide helpful information for the engineering application of anammox.
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Affiliation(s)
- Qi Zhang
- College of the Environment & Ecology, Xiamen University, South Xiang'an Road, Xiang'an District, Xiamen, Fujian 361102, China
| | - Jih-Gaw Lin
- College of the Environment & Ecology, Xiamen University, South Xiang'an Road, Xiang'an District, Xiamen, Fujian 361102, China; Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Zhe Kong
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Yanlong Zhang
- College of the Environment & Ecology, Xiamen University, South Xiang'an Road, Xiang'an District, Xiamen, Fujian 361102, China.
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Wang Q, Zhou YM, Xing CY, Li WC, Shen Y, Yan P, Guo JS, Fang F, Chen YP. Encapsulins from Ca. Brocadia fulgida: An effective tool to enhance the tolerance of engineered bacteria (pET-28a-cEnc) to Zn 2. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:128954. [PMID: 35462189 DOI: 10.1016/j.jhazmat.2022.128954] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Zn2+ is largely discharged from many industries and poses a severe threat to the environment, making its remediation crucial. Encapsulins, proteinaceous nano-compartments, may protect cells against environmental stresses by sequestering toxic substances. To determine whether hemerythrin-containing encapsulins (cEnc) from anammox bacteria Ca. Brocadia fulgida can help cells deal with toxic substances such as Zn2+, we transferred cEnc into E.coli by molecular biology technologies for massive expression and then cultured them in media with increasing Zn2+ levels. The engineered bacteria (with cEnc) grew better and entered the apoptosis phase later, while wild bacteria showed poor survival. Furthermore, tandem mass tag-based quantitative proteomic analysis was used to reveal the underlying regulatory mechanism by which the genetically-engineered bacteria (with cEnc) adapted to Zn2+ stress. When Zn2+ was sequestered in cEnc as a transition, the engineered bacteria presented a complex network of regulatory systems against Zn2+-induced cytotoxicity, including functions related to ribosomes, sulfur metabolism, flagellar assembly, DNA repair, protein synthesis, and Zn2+ efflux. Our findings offer an effective and promising stress control strategy to enhance the Zn2+ tolerance of bacteria for Zn2+ remediation and provide a new application for encapsulins.
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Affiliation(s)
- Que Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yue-Ming Zhou
- National Base of International Science and Technology Cooperation for Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Chong-Yang Xing
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligence Technology, Chinese Academy of Sciences, Chongqing 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wen-Chao Li
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yu Shen
- National Base of International Science and Technology Cooperation for Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
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Andreas MP, Giessen TW. Heterologous expression and purification of encapsulins in Streptomyces coelicolor. MethodsX 2022; 9:101787. [PMID: 35898614 PMCID: PMC9309400 DOI: 10.1016/j.mex.2022.101787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/11/2022] [Indexed: 01/31/2023] Open
Abstract
In recent years a large number of encapsulin nanocompartment-encoding operons have been identified in bacterial and archaeal genomes. Encapsulin-encoding genes and operons from GC-rich Gram-positive bacteria, particularly of the phylum Actinobacteria, are often difficult to overexpress and purify in a soluble form using standard Escherichia coli expression systems. Here, we present a protocol to heterologously overexpress encapsulin nanocompartments and encapsulin-containing operons in Streptomyces coelicolor. Successful encapsulin production begins with the transfer of a Streptomyces expression plasmid, encoding the gene(s) of interest, via conjugation to the model actinobacterium S. coelicolor. After growing the conjugated S. coelicolor culture to the optimal optical density, protein production is induced by the addition of the inducer thiostrepton, followed by expression in liquid culture for 1-3 days. Cells are lysed and encapsulin proteins purified using ammonium sulfate precipitation and size exclusion chromatography. The method outlined in this protocol can be utilized to improve cargo loading and overall soluble expression of encapsulin systems when compared to expression in E. coli.•Clone an encapsulin-encoding gene or operon into a Streptomyces expression vector.•Transfer the Streptomyces expression vector to S. coelicolor via conjugation.•Heterologously express and purify empty or cargo-loaded encapsulins from S. coelicolor.
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Affiliation(s)
- Michael P. Andreas
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tobias W. Giessen
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA,Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA,Corresponding author at: Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA.
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41
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Condensation and Protection of DNA by the Myxococcus xanthus Encapsulin: A Novel Function. Int J Mol Sci 2022; 23:ijms23147829. [PMID: 35887179 PMCID: PMC9321382 DOI: 10.3390/ijms23147829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/04/2023] Open
Abstract
Encapsulins are protein nanocages capable of harboring smaller proteins (cargo proteins) within their cavity. The function of the encapsulin systems is related to the encapsulated cargo proteins. The Myxococcus xanthus encapsulin (EncA) naturally encapsulates ferritin-like proteins EncB and EncC as cargo, resulting in a large iron storage nanocompartment, able to accommodate up to 30,000 iron atoms per shell. In the present manuscript we describe the binding and protection of circular double stranded DNA (pUC19) by EncA using electrophoretic mobility shift assays (EMSA), atomic force microscopy (AFM), and DNase protection assays. EncA binds pUC19 with an apparent dissociation constant of 0.3 ± 0.1 µM and a Hill coefficient of 1.4 ± 0.1, while EncC alone showed no interaction with DNA. Accordingly, the EncAC complex displayed a similar DNA binding capacity as the EncA protein. The data suggest that initially, EncA converts the plasmid DNA from a supercoiled to a more relaxed form with a beads-on-a-string morphology. At higher concentrations, EncA self-aggregates, condensing the DNA. This process physically protects DNA from enzymatic digestion by DNase I. The secondary structure and thermal stability of EncA and the EncA-pUC19 complex were evaluated using synchrotron radiation circular dichroism (SRCD) spectroscopy. The overall secondary structure of EncA is maintained upon interaction with pUC19 while the melting temperature of the protein (Tm) slightly increased from 76 ± 1 °C to 79 ± 1 °C. Our work reports, for the first time, the in vitro capacity of an encapsulin shell to interact and protect plasmid DNA similarly to other protein nanocages that may be relevant in vivo.
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Abstract
Subcellular compartmentalization is a defining feature of all cells. In prokaryotes, compartmentalization is generally achieved via protein-based strategies. The two main classes of microbial protein compartments are bacterial microcompartments and encapsulin nanocompartments. Encapsulins self-assemble into proteinaceous shells with diameters between 24 and 42 nm and are defined by the viral HK97-fold of their shell protein. Encapsulins have the ability to encapsulate dedicated cargo proteins, including ferritin-like proteins, peroxidases, and desulfurases. Encapsulation is mediated by targeting sequences present in all cargo proteins. Encapsulins are found in many bacterial and archaeal phyla and have been suggested to play roles in iron storage, stress resistance, sulfur metabolism, and natural product biosynthesis. Phylogenetic analyses indicate that they share a common ancestor with viral capsid proteins. Many pathogens encode encapsulins, and recent evidence suggests that they may contribute toward pathogenicity. The existing information on encapsulin structure, biochemistry, biological function, and biomedical relevance is reviewed here.
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Affiliation(s)
- Tobias W. Giessen
- Departments of Biomedical Engineering and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Gabashvili AN, Efremova MV, Vodopyanov SS, Chmelyuk NS, Oda VV, Sarkisova VA, Leonova MK, Semkina AS, Ivanova AV, Abakumov MA. New Approach to Non-Invasive Tumor Model Monitoring via Self-Assemble Iron Containing Protein Nanocompartments. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:1657. [PMID: 35630878 PMCID: PMC9145190 DOI: 10.3390/nano12101657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/29/2022] [Accepted: 05/09/2022] [Indexed: 02/04/2023]
Abstract
According to the World Health Organization, breast cancer is the most common oncological disease worldwide. There are multiple animal models for different types of breast carcinoma, allowing the research of tumor growth, metastasis, and angiogenesis. When studying these processes, it is crucial to visualize cancer cells for a prolonged time via a non-invasive method, for example, magnetic resonance imaging (MRI). In this study, we establish a new genetically encoded material based on Quasibacillus thermotolerans (Q.thermotolerans, Qt) encapsulin, stably expressed in mouse 4T1 breast carcinoma cells. The label consists of a protein shell containing an enzyme called ferroxidase. When adding Fe2+, a ferroxidase oxidizes Fe2+ to Fe3+, followed by iron oxide nanoparticles formation. Additionally, genes encoding mZip14 metal transporter, enhancing the iron transport, were inserted into the cells via lentiviral transduction. The expression of transgenic sequences does not affect cell viability, and the presence of magnetic nanoparticles formed inside encapsulins results in an increase in T2 relaxivity.
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Affiliation(s)
- Anna N. Gabashvili
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (S.S.V.); (N.S.C.); (V.V.O.); (M.K.L.); (A.V.I.)
- Transplantation Immunology Laboratory, Biomedical Technology Department, National Medical Research Center for Hematology, Novy Zykovsky Drive, 4A, 125167 Moscow, Russia
| | - Maria V. Efremova
- Department of Chemistry and TUM School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany;
- Institute for Synthetic Biomedicine, Helmholtz Zentrum München GmbH, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
- Department of Applied Physics, Eindhoven University of Technology, Cascade P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Stepan S. Vodopyanov
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (S.S.V.); (N.S.C.); (V.V.O.); (M.K.L.); (A.V.I.)
- Biology Faculty, Lomonosov Moscow State University, Leninskiy Gory, 119234 Moscow, Russia;
| | - Nelly S. Chmelyuk
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (S.S.V.); (N.S.C.); (V.V.O.); (M.K.L.); (A.V.I.)
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, Ostrovityanova St., 1, 117997 Moscow, Russia;
| | - Vera V. Oda
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (S.S.V.); (N.S.C.); (V.V.O.); (M.K.L.); (A.V.I.)
| | - Viktoria A. Sarkisova
- Biology Faculty, Lomonosov Moscow State University, Leninskiy Gory, 119234 Moscow, Russia;
- Cell Proliferation Laboratory, Engelhardt Institute of Molecular Biology, Vavilova Street, 32, 119991 Moscow, Russia
| | - Maria K. Leonova
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (S.S.V.); (N.S.C.); (V.V.O.); (M.K.L.); (A.V.I.)
| | - Alevtina S. Semkina
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, Ostrovityanova St., 1, 117997 Moscow, Russia;
- Department of Basic and Applied Neurobiology, Serbsky National Medical Research Center for Psychiatry and Narcology, Kropotkinskiy Per. 23, 119991 Moscow, Russia
| | - Anna V. Ivanova
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (S.S.V.); (N.S.C.); (V.V.O.); (M.K.L.); (A.V.I.)
| | - Maxim A. Abakumov
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (S.S.V.); (N.S.C.); (V.V.O.); (M.K.L.); (A.V.I.)
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, Ostrovityanova St., 1, 117997 Moscow, Russia;
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Edwardson TGW, Levasseur MD, Tetter S, Steinauer A, Hori M, Hilvert D. Protein Cages: From Fundamentals to Advanced Applications. Chem Rev 2022; 122:9145-9197. [PMID: 35394752 DOI: 10.1021/acs.chemrev.1c00877] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.
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Affiliation(s)
| | | | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mao Hori
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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45
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Benler S, Koonin EV. Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes. Front Mol Biosci 2022; 9:821197. [PMID: 35402511 PMCID: PMC8987985 DOI: 10.3389/fmolb.2022.821197] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
Prokaryotic genomes are replete with mobile genetic elements (MGE) that span a continuum of replication autonomy. On numerous occasions during microbial evolution, diverse MGE lose their autonomy altogether but, rather than being quickly purged from the host genome, assume a new function that benefits the host, rendering the immobilized MGE subject to purifying selection, and resulting in its vertical inheritance. This mini-review highlights the diversity of the repurposed (exapted) MGE as well as the plethora of cellular functions that they perform. The principal contribution of the exaptation of MGE and their components is to the prokaryotic functional systems involved in biological conflicts, and in particular, defense against viruses and other MGE. This evolutionary entanglement between MGE and defense systems appears to stem both from mechanistic similarities and from similar evolutionary predicaments whereby both MGEs and defense systems tend to incur fitness costs to the hosts and thereby evolve mechanisms for survival including horizontal mobility, causing host addiction, and exaptation for functions beneficial to the host. The examples discussed demonstrate that the identity of an MGE, overall mobility and relationship with the host cell (mutualistic, symbiotic, commensal, or parasitic) are all factors that affect exaptation.
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46
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Eren E, Wang B, Winkler DC, Watts NR, Steven AC, Wingfield PT. Structural characterization of the Myxococcus xanthus encapsulin and ferritin-like cargo system gives insight into its iron storage mechanism. Structure 2022; 30:551-563.e4. [PMID: 35150605 PMCID: PMC8995368 DOI: 10.1016/j.str.2022.01.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/22/2021] [Accepted: 01/18/2022] [Indexed: 10/19/2022]
Abstract
Encapsulins are bacterial organelle-like cages involved in various aspects of metabolism, especially protection from oxidative stress. They can serve as vehicles for a wide range of medical applications. Encapsulin shell proteins are structurally similar to HK97 bacteriophage capsid protein and their function depends on the encapsulated cargos. The Myxococcus xanthus encapsulin system comprises EncA and three cargos: EncB, EncC, and EncD. EncB and EncC are similar to bacterial ferritins that can oxidize Fe+2 to less toxic Fe+3. We analyzed EncA, EncB, and EncC by cryo-EM and X-ray crystallography. Cryo-EM shows that EncA cages can have T = 3 and T = 1 symmetry and that EncA T = 1 has a unique protomer arrangement. Also, we define EncB and EncC binding sites on EncA. X-ray crystallography of EncB and EncC reveals conformational changes at the ferroxidase center and additional metal binding sites, suggesting a mechanism for Fe oxidation and storage within the encapsulin shell.
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47
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Ross J, McIver Z, Lambert T, Piergentili C, Bird JE, Gallagher KJ, Cruickshank FL, James P, Zarazúa-Arvizu E, Horsfall LE, Waldron KJ, Wilson MD, Mackay CL, Baslé A, Clarke DJ, Marles-Wright J. Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment. SCIENCE ADVANCES 2022; 8:eabj4461. [PMID: 35080974 PMCID: PMC8791618 DOI: 10.1126/sciadv.abj4461] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Encapsulins are protein nanocompartments that house various cargo enzymes, including a family of decameric ferritin-like proteins. Here, we study a recombinant Haliangium ochraceum encapsulin:encapsulated ferritin complex using cryo-electron microscopy and hydrogen/deuterium exchange mass spectrometry to gain insight into the structural relationship between the encapsulin shell and its protein cargo. An asymmetric single-particle reconstruction reveals four encapsulated ferritin decamers in a tetrahedral arrangement within the encapsulin nanocompartment. This leads to a symmetry mismatch between the protein cargo and the icosahedral encapsulin shell. The encapsulated ferritin decamers are offset from the interior face of the encapsulin shell. Using hydrogen/deuterium exchange mass spectrometry, we observed the dynamic behavior of the major fivefold pore in the encapsulin shell and show the pore opening via the movement of the encapsulin A-domain. These data will accelerate efforts to engineer the encapsulation of heterologous cargo proteins and to alter the permeability of the encapsulin shell via pore modifications.
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Affiliation(s)
- Jennifer Ross
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Zak McIver
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Thomas Lambert
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Cecilia Piergentili
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jasmine Emma Bird
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Kelly J. Gallagher
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Faye L. Cruickshank
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Patrick James
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Louise E. Horsfall
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kevin J. Waldron
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Marcus D. Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - C. Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Arnaud Baslé
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - David J. Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Jon Marles-Wright
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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48
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Wiryaman T, Toor N. Recent advances in the structural biology of encapsulin bacterial nanocompartments. J Struct Biol X 2022; 6:100062. [PMID: 35146412 PMCID: PMC8802124 DOI: 10.1016/j.yjsbx.2022.100062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 02/05/2023] Open
Abstract
Large capsid-like nanocompartments called encapsulins are common in bacteria and archaea and contain cargo proteins with diverse functions. Advances in cryo-electron microscopy have enabled structure determination of many encapsulins in recent years. Here we summarize findings from recent encapsulin structures that have significant implications for their biological roles. We also compare important features such as the E-loop, cargo-peptide binding site, and the fivefold axis channel in different structures. In addition, we describe the discovery of a flavin-binding pocket within the encapsulin shell that may reveal a role for this nanocompartment in iron metabolism.
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Affiliation(s)
| | - Navtej Toor
- University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
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49
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Boyton I, Goodchild SC, Diaz D, Elbourne A, Collins-Praino LE, Care A. Characterizing the Dynamic Disassembly/Reassembly Mechanisms of Encapsulin Protein Nanocages. ACS OMEGA 2022; 7:823-836. [PMID: 35036749 PMCID: PMC8757444 DOI: 10.1021/acsomega.1c05472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/19/2021] [Indexed: 05/22/2023]
Abstract
Encapsulins, self-assembling icosahedral protein nanocages derived from prokaryotes, represent a versatile set of tools for nanobiotechnology. However, a comprehensive understanding of the mechanisms underlying encapsulin self-assembly, disassembly, and reassembly is lacking. Here, we characterize the disassembly/reassembly properties of three encapsulin nanocages that possess different structural architectures: T = 1 (24 nm), T = 3 (32 nm), and T = 4 (42 nm). Using spectroscopic techniques and electron microscopy, encapsulin architectures were found to exhibit varying sensitivities to the denaturant guanidine hydrochloride (GuHCl), extreme pH, and elevated temperature. While all three encapsulins showed the capacity to reassemble following GuHCl-induced disassembly (within 75 min), only the smallest T = 1 nanocage reassembled after disassembly in basic pH (within 15 min). Furthermore, atomic force microscopy revealed that all encapsulins showed a significant loss of structural integrity after undergoing sequential disassembly/reassembly steps. These findings provide insights into encapsulins' disassembly/reassembly dynamics, thus informing their future design, modification, and application.
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Affiliation(s)
- India Boyton
- School
of Life Sciences, University of Technology
Sydney, Ultimo, New South Wales 2007, Australia
- ARC
Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Macquarie
Park, New South Wales 2109, Australia
| | - Sophia C. Goodchild
- Department
of Molecular Sciences, Macquarie University, Macquarie Park, New South
Wales 2109, Australia
| | - Dennis Diaz
- Department
of Molecular Sciences, Macquarie University, Macquarie Park, New South
Wales 2109, Australia
| | - Aaron Elbourne
- School
of Science, College of Science, Engineering and Health, RMIT University, Melbourne, Victoria 3000, Australia
| | - Lyndsey E. Collins-Praino
- Adelaide
Medical School, The University of Adelaide, Adelaide, South Australia 5005, Australia
- ARC
Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Macquarie
Park, New South Wales 2109, Australia
| | - Andrew Care
- School
of Life Sciences, University of Technology
Sydney, Ultimo, New South Wales 2007, Australia
- ARC
Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Macquarie
Park, New South Wales 2109, Australia
- ARC Centre
of Excellence in Synthetic Biology, Macquarie
University, Macquarie Park, New South Wales 2109, Australia
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50
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Furukawa H, Inaba H, Sasaki Y, Akiyoshi K, Matsuura K. Embedding a membrane protein into an enveloped artificial viral replica. RSC Chem Biol 2022; 3:231-241. [PMID: 35360888 PMCID: PMC8827153 DOI: 10.1039/d1cb00166c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/20/2021] [Indexed: 12/20/2022] Open
Abstract
Natural enveloped viruses, in which nucleocapsids are covered with lipid bilayers, contain membrane proteins on the outer surface that are involved in diverse functions, such as adhesion and infection of host cells. Previously, we constructed an enveloped artificial viral capsid through the complexation of cationic lipid bilayers onto an anionic artificial viral capsid self-assembled from β-annulus peptides. Here we demonstrate the embedding of the membrane protein Connexin-43 (Cx43), on the enveloped artificial viral capsid using a cell-free expression system. The expression of Cx43 in the presence of the enveloped artificial viral capsid was confirmed by western blot analysis. The embedding of Cx43 on the envelope was evaluated by detection via the anti-Cx43 antibody, using fluorescence correlation spectroscopy (FCS) and transmission electron microscopy (TEM). Interestingly, many spherical structures connected to each other were observed in TEM images of the Cx43-embedded enveloped viral replica. In addition, it was shown that fluorescent dyes could be selectively transported from Cx43-embedded enveloped viral replicas into Cx43-expressing HepG2 cells. This study provides a proof of concept for the creation of multimolecular crowding complexes, that is, an enveloped artificial viral replica embedded with membrane proteins. We demonstrate the embedding membrane protein, Cx43, on the enveloped artificial viral capsid using a cell-free expression system. The embedding of Cx43 on the envelope was evaluated by detection with anti-Cx43 antibody using FCS and TEM.![]()
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Affiliation(s)
- Hiroto Furukawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
| | - Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori 680-8552, Japan
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