51
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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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52
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Koonin EV, Dolja VV, Krupovic M, Kuhn JH. Viruses Defined by the Position of the Virosphere within the Replicator Space. Microbiol Mol Biol Rev 2021; 85:e0019320. [PMID: 34468181 PMCID: PMC8483706 DOI: 10.1128/mmbr.00193-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Originally, viruses were defined as miniscule infectious agents that passed through filters that retain even the smallest cells. Subsequently, viruses were considered obligate intracellular parasites whose reproduction depends on their cellular hosts for energy supply and molecular building blocks. However, these features are insufficient to unambiguously define viruses as they are broadly understood today. We outline possible approaches to define viruses and explore the boundaries of the virosphere within the virtual space of replicators and the relationships between viruses and other types of replicators. Regardless of how, exactly, viruses are defined, viruses clearly have evolved on many occasions from nonviral replicators, such as plasmids, by recruiting host proteins to become virion components. Conversely, other types of replicators have repeatedly evolved from viruses. Thus, the virosphere is a dynamic entity with extensive evolutionary traffic across its boundaries. We argue that the virosphere proper, here termed orthovirosphere, consists of a distinct variety of replicators that encode structural proteins encasing the replicators' genomes, thereby providing protection and facilitating transmission among hosts. Numerous and diverse replicators, such as virus-derived but capsidless RNA and DNA elements, or defective viruses occupy the zone surrounding the orthovirosphere in the virtual replicator space. We define this zone as the perivirosphere. Although intense debates on the nature of certain replicators that adorn the internal and external boundaries of the virosphere will likely continue, we present an operational definition of virus that recently has been accepted by the International Committee on Taxonomy of Viruses.
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Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerian V. Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
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53
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The development of natural and designed protein nanocages for encapsulation and delivery of active compounds. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.107004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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54
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Almeida AV, Carvalho AJ, Pereira AS. Encapsulin nanocages: Protein encapsulation and iron sequestration. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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55
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Jones JA, Cristie-David AS, Andreas MP, Giessen TW. Triggered Reversible Disassembly of an Engineered Protein Nanocage*. Angew Chem Int Ed Engl 2021; 60:25034-25041. [PMID: 34532937 PMCID: PMC8578439 DOI: 10.1002/anie.202110318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Indexed: 01/13/2023]
Abstract
Protein nanocages play crucial roles in sub-cellular compartmentalization and spatial control in all domains of life and have been used as biomolecular tools for applications in biocatalysis, drug delivery, and bionanotechnology. The ability to control their assembly state under physiological conditions would further expand their practical utility. To gain such control, we introduced a peptide capable of triggering conformational change at a key structural position in the largest known encapsulin nanocompartment. We report the structure of the resulting engineered nanocage and demonstrate its ability to disassemble and reassemble on demand under physiological conditions. We demonstrate its capacity for in vivo encapsulation of proteins of choice while also demonstrating in vitro cargo loading capabilities. Our results represent a functionally robust addition to the nanocage toolbox and a novel approach for controlling protein nanocage disassembly and reassembly under mild conditions.
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Affiliation(s)
- Jesse A Jones
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, 1150 W. Medical Center Dr., MSRB2, Ann Arbor, MI, 48109-5622, USA
| | - Ajitha S Cristie-David
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, 1150 W. Medical Center Dr., MSRB2, Ann Arbor, MI, 48109-5622, USA
| | - Michael P Andreas
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, 1150 W. Medical Center Dr., MSRB2, Ann Arbor, MI, 48109-5622, USA
| | - Tobias W Giessen
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, 1150 W. Medical Center Dr., MSRB2, Ann Arbor, MI, 48109-5622, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, 1150 W. Medical Center Dr., MSRB2, Ann Arbor, MI, 48109-5622, USA
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56
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Jones JA, Cristie‐David AS, Andreas MP, Giessen TW. Triggered Reversible Disassembly of an Engineered Protein Nanocage**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jesse A. Jones
- Department of Biomedical Engineering University of Michigan Medical School, Ann Arbor 1150 W. Medical Center Dr., MSRB2 Ann Arbor MI 48109-5622 USA
| | - Ajitha S. Cristie‐David
- Department of Biomedical Engineering University of Michigan Medical School, Ann Arbor 1150 W. Medical Center Dr., MSRB2 Ann Arbor MI 48109-5622 USA
| | - Michael P. Andreas
- Department of Biomedical Engineering University of Michigan Medical School, Ann Arbor 1150 W. Medical Center Dr., MSRB2 Ann Arbor MI 48109-5622 USA
| | - Tobias W. Giessen
- Department of Biomedical Engineering University of Michigan Medical School, Ann Arbor 1150 W. Medical Center Dr., MSRB2 Ann Arbor MI 48109-5622 USA
- Department of Biological Chemistry University of Michigan Medical School, Ann Arbor 1150 W. Medical Center Dr., MSRB2 Ann Arbor MI 48109-5622 USA
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57
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Lien KA, Dinshaw K, Nichols RJ, Cassidy-Amstutz C, Knight M, Singh R, Eltis LD, Savage DF, Stanley SA. A nanocompartment system contributes to defense against oxidative stress in Mycobacterium tuberculosis. eLife 2021; 10:e74358. [PMID: 34751132 PMCID: PMC8635971 DOI: 10.7554/elife.74358] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/06/2021] [Indexed: 01/18/2023] Open
Abstract
Encapsulin nanocompartments are an emerging class of prokaryotic protein-based organelle consisting of an encapsulin protein shell that encloses a protein cargo. Genes encoding nanocompartments are widespread in bacteria and archaea, and recent works have characterized the biochemical function of several cargo enzymes. However, the importance of these organelles to host physiology is poorly understood. Here, we report that the human pathogen Mycobacterium tuberculosis (Mtb) produces a nanocompartment that contains the dye-decolorizing peroxidase DyP. We show that this nanocompartment is important for the ability of Mtb to resist oxidative stress in low pH environments, including during infection of host cells and upon treatment with a clinically relevant antibiotic. Our findings are the first to implicate a nanocompartment in bacterial pathogenesis and reveal a new mechanism that Mtb uses to combat oxidative stress.
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Affiliation(s)
- Katie A Lien
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
| | - Kayla Dinshaw
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
| | - Robert J Nichols
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Caleb Cassidy-Amstutz
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Matthew Knight
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Rahul Singh
- Department of Microbiology and Immunology, The University of British ColumbiaVancouverCanada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, The University of British ColumbiaVancouverCanada
| | - David F Savage
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Sarah A Stanley
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, BerkeleyBerkeleyUnited States
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58
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Lohner P, Zmyslia M, Thurn J, Pape JK, Gerasimaitė R, Keller‐Findeisen J, Groeer S, Deuringer B, Süss R, Walther A, Hell SW, Lukinavičius G, Hugel T, Jessen‐Trefzer C. Inside a Shell—Organometallic Catalysis Inside Encapsulin Nanoreactors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Philipp Lohner
- Department of Pharmaceutical Biology and Biotechnology University of Freiburg Stefan-Meier-Str. 19 79104 Freiburg Germany
| | - Mariia Zmyslia
- Department of Pharmaceutical Biology and Biotechnology University of Freiburg Stefan-Meier-Str. 19 79104 Freiburg Germany
| | - Johann Thurn
- Institute of Physical Chemistry II University of Freiburg Albertstr. 21 79104 Freiburg Germany
| | - Jasmin K. Pape
- Department of NanoBiophotonics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Goettingen Germany
| | - Rūta Gerasimaitė
- Chromatin Labeling and Imaging Group Department of NanoBiophotonics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
| | - Jan Keller‐Findeisen
- Department of NanoBiophotonics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Goettingen Germany
| | - Saskia Groeer
- Institute for Macromolecular Chemistry A3BMS Lab: Adaptive, Active and Autonomous Bioinspired Material Systems University of Freiburg Stefan-Meier-Str. 31, Hermann Staudinger Building 79104 Freiburg Germany
| | - Benedikt Deuringer
- Department of Pharmaceutical Technology and Biopharmacy University of Freiburg Sonnenstraße 5 79104 Freiburg Germany
| | - Regine Süss
- Department of Pharmaceutical Technology and Biopharmacy University of Freiburg Sonnenstraße 5 79104 Freiburg Germany
| | - Andreas Walther
- Cluster of Excellence livMatS @ FIT–Freiburg Center for Interactive Materials and Bioinspired Technologies Georges-Köhler-Allee 105 79110 Freiburg Germany
- Department of Chemistry, A3BMS Lab University of Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Stefan W. Hell
- Department of NanoBiophotonics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Goettingen Germany
- Department of Optical Nanoscopy Max Planck Institute for Medical Research Jahnstraße 29 69120 Heidelberg Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group Department of NanoBiophotonics Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry II University of Freiburg Albertstr. 21 79104 Freiburg Germany
- Cluster of Excellence livMatS @ FIT–Freiburg Center for Interactive Materials and Bioinspired Technologies Georges-Köhler-Allee 105 79110 Freiburg Germany
| | - Claudia Jessen‐Trefzer
- Department of Pharmaceutical Biology and Biotechnology University of Freiburg Stefan-Meier-Str. 19 79104 Freiburg Germany
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59
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Lohner P, Zmyslia M, Thurn J, Pape JK, Gerasimaitė R, Keller‐Findeisen J, Groeer S, Deuringer B, Süss R, Walther A, Hell SW, Lukinavičius G, Hugel T, Jessen‐Trefzer C. Inside a Shell-Organometallic Catalysis Inside Encapsulin Nanoreactors. Angew Chem Int Ed Engl 2021; 60:23835-23841. [PMID: 34418246 PMCID: PMC8596989 DOI: 10.1002/anie.202110327] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Indexed: 01/23/2023]
Abstract
Compartmentalization of chemical reactions inside cells are a fundamental requirement for life. Encapsulins are self-assembling protein-based nanocompartments from the prokaryotic repertoire that present a highly attractive platform for intracellular compartmentalization of chemical reactions by design. Using single-molecule Förster resonance energy transfer and 3D-MINFLUX analysis, we analyze fluorescently labeled encapsulins on a single-molecule basis. Furthermore, by equipping these capsules with a synthetic ruthenium catalyst via covalent attachment to a non-native host protein, we are able to perform in vitro catalysis and go on to show that engineered encapsulins can be used as hosts for transition metal catalysis inside living cells in confined space.
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Affiliation(s)
- Philipp Lohner
- Department of Pharmaceutical Biology and BiotechnologyUniversity of FreiburgStefan-Meier-Str. 1979104FreiburgGermany
| | - Mariia Zmyslia
- Department of Pharmaceutical Biology and BiotechnologyUniversity of FreiburgStefan-Meier-Str. 1979104FreiburgGermany
| | - Johann Thurn
- Institute of Physical Chemistry IIUniversity of FreiburgAlbertstr. 2179104FreiburgGermany
| | - Jasmin K. Pape
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GoettingenGermany
| | - Rūta Gerasimaitė
- Chromatin Labeling and Imaging GroupDepartment of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Jan Keller‐Findeisen
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GoettingenGermany
| | - Saskia Groeer
- Institute for Macromolecular ChemistryA3BMS Lab: Adaptive, Active and Autonomous Bioinspired Material SystemsUniversity of FreiburgStefan-Meier-Str. 31, Hermann Staudinger Building79104FreiburgGermany
| | - Benedikt Deuringer
- Department of Pharmaceutical Technology and BiopharmacyUniversity of FreiburgSonnenstraße 579104FreiburgGermany
| | - Regine Süss
- Department of Pharmaceutical Technology and BiopharmacyUniversity of FreiburgSonnenstraße 579104FreiburgGermany
| | - Andreas Walther
- Cluster of Excellence livMatS @ FIT–Freiburg Center for Interactive Materials and Bioinspired TechnologiesGeorges-Köhler-Allee 10579110FreiburgGermany
- Department of Chemistry, A3BMS LabUniversity of MainzDuesbergweg 10–1455128MainzGermany
| | - Stefan W. Hell
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GoettingenGermany
- Department of Optical NanoscopyMax Planck Institute for Medical ResearchJahnstraße 2969120HeidelbergGermany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging GroupDepartment of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Thorsten Hugel
- Institute of Physical Chemistry IIUniversity of FreiburgAlbertstr. 2179104FreiburgGermany
- Cluster of Excellence livMatS @ FIT–Freiburg Center for Interactive Materials and Bioinspired TechnologiesGeorges-Köhler-Allee 10579110FreiburgGermany
| | - Claudia Jessen‐Trefzer
- Department of Pharmaceutical Biology and BiotechnologyUniversity of FreiburgStefan-Meier-Str. 1979104FreiburgGermany
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60
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Abstract
Increasing efficiency is an important driving force behind cellular organization and often achieved through compartmentalization. Long recognized as a core principle of eukaryotic cell organization, its widespread occurrence in prokaryotes has only recently come to light. Despite the early discovery of a few microcompartments such as gas vesicles and carboxysomes, the vast majority of these structures in prokaryotes are less than 100 nm in diameter - too small for conventional light microscopy and electron microscopic thin sectioning. Consequently, these smaller-sized nanocompartments have therefore been discovered serendipitously and then through bioinformatics shown to be broadly distributed. Their small uniform size, robust self-assembly, high stability, excellent biocompatibility, and large cargo capacity make them excellent candidates for biotechnology applications. This review will highlight our current knowledge of nanocompartments, the prospects for applications as well as open question and challenges that need to be addressed to fully understand these important structures.
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61
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Lučić M, Wilson MT, Svistunenko DA, Owen RL, Hough MA, Worrall JAR. Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of Fe IV = O formation in bacterial dye-decolorizing peroxidases. J Biol Inorg Chem 2021; 26:743-761. [PMID: 34477969 PMCID: PMC8463360 DOI: 10.1007/s00775-021-01896-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/23/2021] [Indexed: 11/26/2022]
Abstract
Structure determination of proteins and enzymes by X-ray crystallography remains the most widely used approach to complement functional and mechanistic studies. Capturing the structures of intact redox states in metalloenzymes is critical for assigning the chemistry carried out by the metal in the catalytic cycle. Unfortunately, X-rays interact with protein crystals to generate solvated photoelectrons that can reduce redox active metals and hence change the coordination geometry and the coupled protein structure. Approaches to mitigate such site-specific radiation damage continue to be developed, but nevertheless application of such approaches to metalloenzymes in combination with mechanistic studies are often overlooked. In this review, we summarize our recent structural and kinetic studies on a set of three heme peroxidases found in the bacterium Streptomyces lividans that each belong to the dye decolourizing peroxidase (DyP) superfamily. Kinetically, each of these DyPs has a distinct reactivity with hydrogen peroxide. Through a combination of low dose synchrotron X-ray crystallography and zero dose serial femtosecond X-ray crystallography using an X-ray free electron laser (XFEL), high-resolution structures with unambiguous redox state assignment of the ferric and ferryl (FeIV = O) heme species have been obtained. Experiments using stopped-flow kinetics, solvent-isotope exchange and site-directed mutagenesis with this set of redox state validated DyP structures have provided the first comprehensive kinetic and structural framework for how DyPs can modulate their distal heme pocket Asp/Arg dyad to use either the Asp or the Arg to facilitate proton transfer and rate enhancement of peroxide heterolysis.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, Oxfordshire, UK
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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62
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Van de Steen A, Khalife R, Colant N, Mustafa Khan H, Deveikis M, Charalambous S, Robinson CM, Dabas R, Esteban Serna S, Catana DA, Pildish K, Kalinovskiy V, Gustafsson K, Frank S. Bioengineering bacterial encapsulin nanocompartments as targeted drug delivery system. Synth Syst Biotechnol 2021; 6:231-241. [PMID: 34541345 PMCID: PMC8435816 DOI: 10.1016/j.synbio.2021.09.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 11/21/2022] Open
Abstract
The development of Drug Delivery Systems (DDS) has led to increasingly efficient therapies for the treatment and detection of various diseases. DDS use a range of nanoscale delivery platforms produced from polymeric of inorganic materials, such as micelles, and metal and polymeric nanoparticles, but their variant chemical composition make alterations to their size, shape, or structures inherently complex. Genetically encoded protein nanocages are highly promising DDS candidates because of their modular composition, ease of recombinant production in a range of hosts, control over assembly and loading of cargo molecules and biodegradability. One example of naturally occurring nanocompartments are encapsulins, recently discovered bacterial organelles that have been shown to be reprogrammable as nanobioreactors and vaccine candidates. Here we report the design and application of a targeted DDS platform based on the Thermotoga maritima encapsulin reprogrammed to display an antibody mimic protein called Designed Ankyrin repeat protein (DARPin) on the outer surface and to encapsulate a cytotoxic payload. The DARPin9.29 chosen in this study specifically binds to human epidermal growth factor receptor 2 (HER2) on breast cancer cells, as demonstrated in an in vitro cell culture model. The encapsulin-based DDS is assembled in one step in vivo by co-expressing the encapsulin-DARPin9.29 fusion protein with an engineered flavin-binding protein mini-singlet oxygen generator (MiniSOG), from a single plasmid in Escherichia coli. Purified encapsulin-DARPin_miniSOG nanocompartments bind specifically to HER2 positive breast cancer cells and trigger apoptosis, indicating that the system is functional and specific. The DDS is modular and has the potential to form the basis of a multi-receptor targeted system by utilising the DARPin screening libraries, allowing use of new DARPins of known specificities, and through the proven flexibility of the encapsulin cargo loading mechanism, allowing selection of cargo proteins of choice.
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Key Words
- Annexin V-FITC, Annexin V-Fluorescein IsoThiocyanate Conjugate
- Cytotoxic protein
- DARPin
- DARPin9.29, Designed Ankyrin Repeat Protein 9.29
- DDS, Drug Delivery System
- Drug delivery system
- EPR, Enhanced Permeability and Retention effect
- Encapsulin
- HER2, Human Epidermal growth factor Receptor 2
- His6, Hexahistidine
- MSCs, Mesenchymal Stem Cells
- NPs, NanoParticles
- SK-BR-3, Sloan-Kettering Breast cancer cell line/HER2-overexpressing human breast cancer cell line
- STII, StrepII-tag, an eight-residue peptide sequence (Trp-Ser-His-Pro-Gln-Phe-Glu-Lys) with intrinsic affinity toward streptavidin that can be fused to recombinant protein in various fashions
- T. maritima, Thermotoga maritima
- VLPs, Virus-Like Particle
- iGEM, international Genetically Engineered Machine
- iLOV, improved Light, Oxygen or Voltage-sensing flavoprotein
- mScarlet, a bright monomeric red fluorescent protein
- miniSOG, mini-Singlet Oxygen Generator
- rTurboGFP, recombinant Turbo Green Fluorescent Protein
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Affiliation(s)
| | - Rana Khalife
- Department of Biochemical Engineering, University College London, UK
| | - Noelle Colant
- Department of Biochemical Engineering, University College London, UK
| | | | - Matas Deveikis
- Department of Biochemical Engineering, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Saverio Charalambous
- Department of Biochemical Engineering, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Clare M. Robinson
- Natural Sciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Rupali Dabas
- Natural Sciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Sofia Esteban Serna
- Division of Biosciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Diana A. Catana
- Division of Biosciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Konstantin Pildish
- Division of Biosciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Vladimir Kalinovskiy
- Division of Biosciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Kenth Gustafsson
- Department of Biochemical Engineering, University College London, UK
| | - Stefanie Frank
- Department of Biochemical Engineering, University College London, UK
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63
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Andreas MP, Giessen TW. Large-scale computational discovery and analysis of virus-derived microbial nanocompartments. Nat Commun 2021; 12:4748. [PMID: 34362927 PMCID: PMC8346489 DOI: 10.1038/s41467-021-25071-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/12/2021] [Indexed: 02/06/2023] Open
Abstract
Encapsulins are a class of microbial protein compartments defined by the viral HK97-fold of their capsid protein, self-assembly into icosahedral shells, and dedicated cargo loading mechanism for sequestering specific enzymes. Encapsulins are often misannotated and traditional sequence-based searches yield many false positive hits in the form of phage capsids. Here, we develop an integrated search strategy to carry out a large-scale computational analysis of prokaryotic genomes with the goal of discovering an exhaustive and curated set of all HK97-fold encapsulin-like systems. We find over 6,000 encapsulin-like systems in 31 bacterial and four archaeal phyla, including two novel encapsulin families. We formulate hypotheses about their potential biological functions and biomedical relevance, which range from natural product biosynthesis and stress resistance to carbon metabolism and anaerobic hydrogen production. An evolutionary analysis of encapsulins and related HK97-type virus families shows that they share a common ancestor, and we conclude that encapsulins likely evolved from HK97-type bacteriophages.
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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.
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Szyszka TN, Jenner EN, Tasneem N, Lau YH. Molecular Display on Protein Nanocompartments: Design Strategies and Systems Applications. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202100025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Taylor N. Szyszka
- School of Chemistry The University of Sydney Eastern Ave Camperdown NSW 2006 Australia
- The University of Sydney Nano Institute Camperdown NSW 2006 Australia
| | - Eric N. Jenner
- School of Chemistry The University of Sydney Eastern Ave Camperdown NSW 2006 Australia
| | - Nuren Tasneem
- School of Chemistry The University of Sydney Eastern Ave Camperdown NSW 2006 Australia
| | - Yu Heng Lau
- School of Chemistry The University of Sydney Eastern Ave Camperdown NSW 2006 Australia
- The University of Sydney Nano Institute Camperdown NSW 2006 Australia
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65
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Oerlemans RAJF, Timmermans SBPE, van Hest JCM. Artificial Organelles: Towards Adding or Restoring Intracellular Activity. Chembiochem 2021; 22:2051-2078. [PMID: 33450141 PMCID: PMC8252369 DOI: 10.1002/cbic.202000850] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/15/2021] [Indexed: 12/15/2022]
Abstract
Compartmentalization is one of the main characteristics that define living systems. Creating a physically separated microenvironment allows nature a better control over biological processes, as is clearly specified by the role of organelles in living cells. Inspired by this phenomenon, researchers have developed a range of different approaches to create artificial organelles: compartments with catalytic activity that add new function to living cells. In this review we will discuss three complementary lines of investigation. First, orthogonal chemistry approaches are discussed, which are based on the incorporation of catalytically active transition metal-containing nanoparticles in living cells. The second approach involves the use of premade hybrid nanoreactors, which show transient function when taken up by living cells. The third approach utilizes mostly genetic engineering methods to create bio-based structures that can be ultimately integrated with the cell's genome to make them constitutively active. The current state of the art and the scope and limitations of the field will be highlighted with selected examples from the three approaches.
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Affiliation(s)
- Roy A. J. F. Oerlemans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Suzanne B. P. E. Timmermans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Jan C. M. van Hest
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
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66
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Rodríguez JM, Allende-Ballestero C, Cornelissen JJLM, Castón JR. Nanotechnological Applications Based on Bacterial Encapsulins. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1467. [PMID: 34206092 PMCID: PMC8229669 DOI: 10.3390/nano11061467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023]
Abstract
Encapsulins are proteinaceous nanocontainers, constructed by a single species of shell protein that self-assemble into 20-40 nm icosahedral particles. Encapsulins are structurally similar to the capsids of viruses of the HK97-like lineage, to which they are evolutionarily related. Nearly all these nanocontainers encase a single oligomeric protein that defines the physiological role of the complex, although a few encapsulate several activities within a single particle. Encapsulins are abundant in bacteria and archaea, in which they participate in regulation of oxidative stress, detoxification, and homeostasis of key chemical elements. These nanocontainers are physically robust, contain numerous pores that permit metabolite flux through the shell, and are very tolerant of genetic manipulation. There are natural mechanisms for efficient functionalization of the outer and inner shell surfaces, and for the in vivo and in vitro internalization of heterologous proteins. These characteristics render encapsulin an excellent platform for the development of biotechnological applications. Here we provide an overview of current knowledge of encapsulin systems, summarize the remarkable toolbox developed by researchers in this field, and discuss recent advances in the biomedical and bioengineering applications of encapsulins.
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Affiliation(s)
- Javier M. Rodríguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
| | - Carolina Allende-Ballestero
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
| | - Jeroen J. L. M. Cornelissen
- Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands;
| | - José R. Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
- Nanobiotechnology Associated Unit CNB-CSIC-IMDEA, Campus Cantoblanco, 28049 Madrid, Spain
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67
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Farhadi A, Sigmund F, Westmeyer GG, Shapiro MG. Genetically encodable materials for non-invasive biological imaging. NATURE MATERIALS 2021; 20:585-592. [PMID: 33526879 PMCID: PMC8606175 DOI: 10.1038/s41563-020-00883-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 11/18/2020] [Indexed: 05/04/2023]
Abstract
Many questions in basic biology and medicine require the ability to visualize the function of specific cells and molecules inside living organisms. In this context, technologies such as ultrasound, optoacoustics and magnetic resonance provide non-invasive imaging access to deep-tissue regions, as used in many laboratories and clinics to visualize anatomy and physiology. In addition, recent work has enabled these technologies to image the location and function of specific cells and molecules inside the body by coupling the physics of sound waves, nuclear spins and light absorption to unique protein-based materials. These materials, which include air-filled gas vesicles, capsid-like nanocompartments, pigment-producing enzymes and transmembrane transporters, enable new forms of biomolecular and cellular contrast. The ability of these protein-based contrast agents to be genetically encoded and produced by cells creates opportunities for unprecedented in vivo studies of cellular function, while their amenability to genetic engineering enables atomic-level design of their physical, chemical and biological properties.
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Affiliation(s)
- Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Felix Sigmund
- Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Synthetic Biomedicine, Helmholtz Zentrum Muenchen, Neuherberg, Germany
| | - Gil Gregor Westmeyer
- Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany.
- Institute for Synthetic Biomedicine, Helmholtz Zentrum Muenchen, Neuherberg, Germany.
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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68
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Wiryaman T, Toor N. Cryo-EM structure of a thermostable bacterial nanocompartment. IUCRJ 2021; 8:342-350. [PMID: 33953921 PMCID: PMC8086157 DOI: 10.1107/s2052252521001949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/18/2021] [Indexed: 05/21/2023]
Abstract
Protein nanocompartments are widespread in bacteria and archaea, but their functions are not yet well understood. Here, the cryo-EM structure of a nanocompartment from the thermophilic bacterium Thermotoga maritima is reported at 2.0 Å resolution. The high resolution of this structure shows that interactions in the E-loop domain may be important for the thermostability of the nanocompartment assembly. Also, the channels at the fivefold axis, threefold axis and dimer interface are assessed for their ability to transport iron. Finally, an unexpected flavin ligand was identified on the exterior of the shell, indicating that this nanocompartment may also play a direct role in iron metabolism.
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Affiliation(s)
- Timothy Wiryaman
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Navtej Toor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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69
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Tang Y, Mu A, Zhang Y, Zhou S, Wang W, Lai Y, Zhou X, Liu F, Yang X, Gong H, Wang Q, Rao Z. Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin. Proc Natl Acad Sci U S A 2021; 118:e2025658118. [PMID: 33853951 PMCID: PMC8072242 DOI: 10.1073/pnas.2025658118] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact and function. Here, we have isolated a native cargo-packaging encapsulin from Mycobacterium smegmatis and determined its complete high-resolution structure by cryogenic electron microscopy (cryo-EM). This encapsulin comprises an icosahedral shell and a dodecameric DyP cargo. The dodecameric DyP consists of two hexamers with a twofold axis of symmetry and stretches across the interior of the encapsulin. Our results reveal that the encapsulin shell plays a role in stabilizing the dodecameric DyP. Furthermore, we have proposed a potential mechanism for removing the hydrogen peroxide based on the structural features. Our study also suggests that the DyP is the primary cargo protein of mycobacterial encapsulins and is a potential target for antituberculosis drug discovery.
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Affiliation(s)
- Yanting Tang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China
| | - An Mu
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yuying Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China
| | - Shan Zhou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 300071 Tianjin, China
| | - Weiwei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Yuezheng Lai
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China
| | - Xiaoting Zhou
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Fengjiang Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Hongri Gong
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China;
| | - Quan Wang
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China;
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 300071 Tianjin, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
- Laboratory of Structural Biology, Tsinghua University, 100084 Beijing, China
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70
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Jenkins MC, Lutz S. Encapsulin Nanocontainers as Versatile Scaffolds for the Development of Artificial Metabolons. ACS Synth Biol 2021; 10:857-869. [PMID: 33769792 DOI: 10.1021/acssynbio.0c00636] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The construction of non-native biosynthetic pathways represents a powerful, modular strategy for the production of valuable synthons and fine chemicals. Accordingly, artificially affixing enzymes that catalyze sequential reactions onto DNAs, proteins, or synthetic scaffolds has proven to be an effective route for generating de novo metabolons with novel functionalities and superior efficiency. In recent years, nanoscale microbial compartments known as encapsulins have emerged as a class of robust and highly engineerable proteinaceous containers with myriad applications in biotechnology and synthetic biology. Herein we report the concurrent surface functionalization and internal packaging of encapsulins from Thermotoga maritima to generate a catalytically competent two-enzyme metabolon. Encapsulins were engineered to covalently sequester up to 60 copies of a dihydrofolate reductase (DHFR) enzyme variant on their exterior surfaces using the SpyCatcher bioconjugation system, while their lumens were packaged with a tetrahydrofolate-dependent demethylase enzyme using short peptide affinity tags abstracted from the encapsulin's native protein cargo. Successful cross-talk between the two colocalized enzymes was confirmed as tetrahydrofolate produced by externally tethered DHFR was capable of driving the demethylation of a lignin-derived aryl substrate by packaged demethylases, albeit slowly. The subsequent introduction of a previously reported pore-enlarging deletion in the encapsulin shell was shown to enhance metabolite exchange such that the encapsulin-based metabolon functioned at speeds equivalent to those of the two enzymes freely dispersed in solution. Our work thus further emphasizes the engineerability of encapsulins and their potential use as flexile scaffolds for biocatalytic applications.
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Affiliation(s)
- Matthew C. Jenkins
- Department of Chemistry, Emory University, Atlanta, Georgia 30084, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30306, United States
| | - Stefan Lutz
- Department of Chemistry, Emory University, Atlanta, Georgia 30084, United States
- Codexis Inc., 200 Penobscot Drive, Redwood City, California 94063, United States
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71
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Nichols RJ, LaFrance B, Phillips NR, Radford DR, Oltrogge LM, Valentin-Alvarado LE, Bischoff AJ, Nogales E, Savage DF. Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism. eLife 2021; 10:e59288. [PMID: 33821786 PMCID: PMC8049743 DOI: 10.7554/elife.59288] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 04/04/2021] [Indexed: 11/13/2022] Open
Abstract
Prokaryotic nanocompartments, also known as encapsulins, are a recently discovered proteinaceous organelle-like compartment in prokaryotes that compartmentalize cargo enzymes. While initial studies have begun to elucidate the structure and physiological roles of encapsulins, bioinformatic evidence suggests that a great diversity of encapsulin nanocompartments remains unexplored. Here, we describe a novel encapsulin in the freshwater cyanobacterium Synechococcus elongatus PCC 7942. This nanocompartment is upregulated upon sulfate starvation and encapsulates a cysteine desulfurase enzyme via an N-terminal targeting sequence. Using cryo-electron microscopy, we have determined the structure of the nanocompartment complex to 2.2 Å resolution. Lastly, biochemical characterization of the complex demonstrated that the activity of the cysteine desulfurase is enhanced upon encapsulation. Taken together, our discovery, structural analysis, and enzymatic characterization of this prokaryotic nanocompartment provide a foundation for future studies seeking to understand the physiological role of this encapsulin in various bacteria.
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Affiliation(s)
- Robert J Nichols
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Benjamin LaFrance
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Naiya R Phillips
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Devon R Radford
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Luis E Valentin-Alvarado
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Amanda J Bischoff
- Department of Chemistry, University of California BerkeleyBerkeleyUnited States
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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72
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Bradley JM, Svistunenko DA, Wilson MT, Hemmings AM, Moore GR, Le Brun NE. Bacterial iron detoxification at the molecular level. J Biol Chem 2021; 295:17602-17623. [PMID: 33454001 PMCID: PMC7762939 DOI: 10.1074/jbc.rev120.007746] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 10/07/2020] [Indexed: 01/18/2023] Open
Abstract
Iron is an essential micronutrient, and, in the case of bacteria, its availability is commonly a growth-limiting factor. However, correct functioning of cells requires that the labile pool of chelatable "free" iron be tightly regulated. Correct metalation of proteins requiring iron as a cofactor demands that such a readily accessible source of iron exist, but overaccumulation results in an oxidative burden that, if unchecked, would lead to cell death. The toxicity of iron stems from its potential to catalyze formation of reactive oxygen species that, in addition to causing damage to biological molecules, can also lead to the formation of reactive nitrogen species. To avoid iron-mediated oxidative stress, bacteria utilize iron-dependent global regulators to sense the iron status of the cell and regulate the expression of proteins involved in the acquisition, storage, and efflux of iron accordingly. Here, we survey the current understanding of the structure and mechanism of the important members of each of these classes of protein. Diversity in the details of iron homeostasis mechanisms reflect the differing nutritional stresses resulting from the wide variety of ecological niches that bacteria inhabit. However, in this review, we seek to highlight the similarities of iron homeostasis between different bacteria, while acknowledging important variations. In this way, we hope to illustrate how bacteria have evolved common approaches to overcome the dual problems of the insolubility and potential toxicity of iron.
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Affiliation(s)
- Justin M Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom.
| | | | - Michael T Wilson
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Andrew M Hemmings
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom; Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Geoffrey R Moore
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom.
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73
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Ochoa JM, Bair K, Holton T, Bobik TA, Yeates TO. MCPdb: The bacterial microcompartment database. PLoS One 2021; 16:e0248269. [PMID: 33780471 PMCID: PMC8007038 DOI: 10.1371/journal.pone.0248269] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
Bacterial microcompartments are organelle-like structures composed entirely of proteins. They have evolved to carry out several distinct and specialized metabolic functions in a wide variety of bacteria. Their outer shell is constructed from thousands of tessellating protein subunits, encapsulating enzymes that carry out the internal metabolic reactions. The shell proteins are varied, with single, tandem and permuted versions of the PF00936 protein family domain comprising the primary structural component of their polyhedral architecture, which is reminiscent of a viral capsid. While considerable amounts of structural and biophysical data have been generated in the last 15 years, the existing functionalities of current resources have limited our ability to rapidly understand the functional and structural properties of microcompartments (MCPs) and their diversity. In order to make the remarkable structural features of bacterial microcompartments accessible to a broad community of scientists and non-specialists, we developed MCPdb: The Bacterial Microcompartment Database (https://mcpdb.mbi.ucla.edu/). MCPdb is a comprehensive resource that categorizes and organizes known microcompartment protein structures and their larger assemblies. To emphasize the critical roles symmetric assembly and architecture play in microcompartment function, each structure in the MCPdb is validated and annotated with respect to: (1) its predicted natural assembly state (2) tertiary structure and topology and (3) the metabolic compartment type from which it derives. The current database includes 163 structures and is available to the public with the anticipation that it will serve as a growing resource for scientists interested in understanding protein-based metabolic organelles in bacteria.
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Affiliation(s)
- Jessica M. Ochoa
- UCLA Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Kaylie Bair
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Thomas Holton
- UCLA Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Thomas A. Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Todd O. Yeates
- UCLA Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
- UCLA Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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74
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Tan YQ, Xue B, Yew WS. Genetically Encodable Scaffolds for Optimizing Enzyme Function. Molecules 2021; 26:molecules26051389. [PMID: 33806660 PMCID: PMC7961827 DOI: 10.3390/molecules26051389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
Enzyme engineering is an indispensable tool in the field of synthetic biology, where enzymes are challenged to carry out novel or improved functions. Achieving these goals sometimes goes beyond modifying the primary sequence of the enzyme itself. The use of protein or nucleic acid scaffolds to enhance enzyme properties has been reported for applications such as microbial production of chemicals, biosensor development and bioremediation. Key advantages of using these assemblies include optimizing reaction conditions, improving metabolic flux and increasing enzyme stability. This review summarizes recent trends in utilizing genetically encodable scaffolds, developed in line with synthetic biology methodologies, to complement the purposeful deployment of enzymes. Current molecular tools for constructing these synthetic enzyme-scaffold systems are also highlighted.
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Affiliation(s)
- Yong Quan Tan
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Bo Xue
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Correspondence: ; Tel.: +65-6516-8624
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75
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Altenburg WJ, Rollins N, Silver PA, Giessen TW. Exploring targeting peptide-shell interactions in encapsulin nanocompartments. Sci Rep 2021; 11:4951. [PMID: 33654191 PMCID: PMC7925596 DOI: 10.1038/s41598-021-84329-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/11/2021] [Indexed: 11/09/2022] Open
Abstract
Encapsulins are recently discovered protein compartments able to specifically encapsulate cargo proteins in vivo. Encapsulation is dependent on C-terminal targeting peptides (TPs). Here, we characterize and engineer TP-shell interactions in the Thermotoga maritima and Myxococcus xanthus encapsulin systems. Using force-field modeling and particle fluorescence measurements we show that TPs vary in native specificity and binding strength, and that TP-shell interactions are determined by hydrophobic and ionic interactions as well as TP flexibility. We design a set of TPs with a variety of predicted binding strengths and experimentally characterize these designs. This yields a set of TPs with novel binding characteristics representing a potentially useful toolbox for future nanoreactor engineering aimed at controlling cargo loading efficiency and the relative stoichiometry of multiple concurrently loaded cargo proteins.
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Affiliation(s)
- Wiggert J Altenburg
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard, Boston, MA, 02115, USA
| | - Nathan Rollins
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard, Boston, MA, 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard, Boston, MA, 02115, USA
| | - Tobias W Giessen
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Wyss Institute for Biologically Inspired Engineering at Harvard, Boston, MA, 02115, USA.
- Department of Biomedical Engineering, 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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76
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Xing CY, Ma TF, Guo JS, Shen Y, Yan P, Fang F, Chen YP. Bacterially self-assembled encapsulin nanocompartment for removing silver from water. WATER RESEARCH 2021; 191:116800. [PMID: 33433335 DOI: 10.1016/j.watres.2020.116800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Compartmentalization can protect cells from the interference of external toxic substances by sequestering toxic products. We hypothesized that proteinaceous nanocompartments may be a feasible candidate material to be added to genetically modified bacteria for the sequestration of toxic environmental products, which would open up a new bioremediation pathway. Here, we showed that the model bacterium (Escherichia coli) with self-assembling nanocompartments can remove silver (Ag) from water. Transmission electron microscopy and energy dispersive X-ray (TEM-EDX) analysis showed that the nanocompartments combined stably with silver in vitro. In addition, when exposed to 30 μM AgNO3, the survival rate of genetically modified bacteria (with nanocompartments) was 86%, while it was just 59% in the wild-type bacteria (without nanocompartments). Label-free quantitative proteomics indicated that the nanocompartments enhanced bacterial activity by inducing the up-regulation of protein processing and secondary metabolites, and decreased their intracellular silver concentration, both of which contributed to their increased resistance to toxic silver. This study on nanocompartments has contributed to a deeper understanding of how bacteria respond to environmental stressors like heavy metal pollutants in water. The technology promises to provide a new strategy for recycling heavy metals from sewage.
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Affiliation(s)
- 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
| | - Teng-Fei Ma
- National Base of International Science and Technology Cooperation for Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China
| | - Jin-Song Guo
- 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
| | - 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 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; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China.
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77
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Diaz D, Vidal X, Sunna A, Care A. Bioengineering a Light-Responsive Encapsulin Nanoreactor: A Potential Tool for In Vitro Photodynamic Therapy. ACS APPLIED MATERIALS & INTERFACES 2021; 13:7977-7986. [PMID: 33586952 DOI: 10.1021/acsami.0c21141] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Encapsulins, a prokaryotic class of self-assembling protein nanocompartments, are being re-engineered to serve as "nanoreactors" for the augmentation or creation of key biochemical reactions. However, approaches that allow encapsulin nanoreactors to be functionally activated with spatial and temporal precision are lacking. We report the construction of a light-responsive encapsulin nanoreactor for "on demand" production of reactive oxygen species (ROS). Herein, encapsulins were loaded with the fluorescent flavoprotein mini-singlet oxygen generator (miniSOG), a biological photosensitizer that is activated by blue light to generate ROS, primarily singlet oxygen (1O2). We established that the nanocompartments stably encased miniSOG and in response to blue light were able to mediate the photoconversion of molecular oxygen into ROS. Using an in vitro model of lung cancer, we showed that ROS generated by the nanoreactor triggered photosensitized oxidation reactions which exerted a toxic effect on tumor cells, suggesting utility in photodynamic therapy. This encapsulin nanoreactor thus represents a platform for the light-controlled initiation and/or modulation of ROS-driven processes in biomedicine and biotechnology.
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Affiliation(s)
- Dennis Diaz
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Xavier Vidal
- Fraunhofer Institut für Angewandte Festkörperphysik (IAF), Tullastrasse 72, 79108 Freiburg, Germany
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia
| | - Andrew Care
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
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78
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Groaz A, Moghimianavval H, Tavella F, Giessen TW, Vecchiarelli AG, Yang Q, Liu AP. Engineering spatiotemporal organization and dynamics in synthetic cells. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 13:e1685. [PMID: 33219745 DOI: 10.1002/wnan.1685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/13/2020] [Accepted: 10/30/2020] [Indexed: 12/28/2022]
Abstract
Constructing synthetic cells has recently become an appealing area of research. Decades of research in biochemistry and cell biology have amassed detailed part lists of components involved in various cellular processes. Nevertheless, recreating any cellular process in vitro in cell-sized compartments remains ambitious and challenging. Two broad features or principles are key to the development of synthetic cells-compartmentalization and self-organization/spatiotemporal dynamics. In this review article, we discuss the current state of the art and research trends in the engineering of synthetic cell membranes, development of internal compartmentalization, reconstitution of self-organizing dynamics, and integration of activities across scales of space and time. We also identify some research areas that could play a major role in advancing the impact and utility of engineered synthetic cells. This article is categorized under: Biology-Inspired Nanomaterials > Lipid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
| | | | | | | | | | - Qiong Yang
- University of Michigan, Ann Arbor, Michigan, USA
| | - Allen P Liu
- University of Michigan, Ann Arbor, Michigan, USA
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79
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Yan Y, Wang W, Wu M, Jetten MSM, Guo J, Ma J, Wang H, Dai X, Wang Y. Transcriptomics Uncovers the Response of Anammox Bacteria to Dissolved Oxygen Inhibition and the Subsequent Recovery Mechanism. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:14674-14685. [PMID: 33147001 DOI: 10.1021/acs.est.0c02842] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Understanding the recovery of anaerobic ammonium-oxidizing (anammox) bacteria after inhibition by dissolved oxygen (DO) is critical for the successful applications of anammox-based processes. Therefore, the effects of oxygen exposure (2 mg L-1 DO for 90 min) and subsequent recovery treatments [N2 purging or nano zero-valent iron (nZVI) addition] on the activity and gene expression in a Kuenenia stuttgartiensis enrichment culture were examined. Combining the self-organizing map clustering and enrichment analysis, we proposed the oxidative stress response of anammox bacteria based on the existing concepts of oxidative stress in microbes: the DO exposure triggered a stringent response in K. stuttgartiensis, which downregulated the transcription levels of genes involved in the central metabolism and diverted energy to a flagellar assembly and metal transport modules; these changes possibly promoted survival during the inhibition of anammox activity. According to the cotranscription with central catabolism genes, putative reactive oxygen species (ROS) scavenger genes (kat and sod) were presumed to detoxify the anammox intermediates rather than ROS. In addition, both activity and mRNA profiles with appropriate amount of nZVI addition (5 and 25 mg L-1) were close to that of control, which proved the effectiveness of nZVI addition in anammox recovery. These results would be relevant to the physio-biochemistry development of anammox bacteria and further enhancement of nitrogen removal in wastewater treatment.
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Affiliation(s)
- Yuan Yan
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
| | - Weigang Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
| | - Mengxiong Wu
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Mike S M Jetten
- Microbiology, IWWR, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, AJ Nijmegen 6525, The Netherlands
| | - Jianhua Guo
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Jie Ma
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
| | - Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
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80
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Horseradish Peroxidase-Decorated Artificial Viral Capsid Constructed from β-Annulus Peptide via Interaction between His-Tag and Ni-NTA. Processes (Basel) 2020. [DOI: 10.3390/pr8111455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Artificial construction of spherical protein assemblies has attracted considerable attention due to its potential use in nanocontainers, nanocarriers, and nanoreactors. In this work, we demonstrate a novel strategy to construct peptide nanocapsules (artificial viral capsids) decorated with enzymes via interactions between His-tag and Ni-NTA. A β-annulus peptide derived from the tomato bushy stunt virus was modified with Ni-NTA at the C-terminus, which is directed toward the exterior surface of the artificial viral capsid. The β-annulus peptide bearing Ni-NTA at the C-terminus self-assembled into capsids of about 50 nm in diameter. The Ni-NTA-displayed capsids were complexed with recombinant horseradish peroxidase (HRP) with a C-terminal His-tag which was expressed in Escherichia coli. The β-annulus peptide-HRP complex formed spherical assemblies whose sizes were 30–90 nm, with the ζ-potential revealing that the HRP was decorated on the outer surface of the capsid.
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81
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Jones JA, Giessen TW. Advances in encapsulin nanocompartment biology and engineering. Biotechnol Bioeng 2020; 118:491-505. [PMID: 32918485 DOI: 10.1002/bit.27564] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/12/2020] [Accepted: 09/09/2020] [Indexed: 12/23/2022]
Abstract
Compartmentalization is an essential feature of all cells. It allows cells to segregate and coordinate physiological functions in a controlled and ordered manner. Different mechanisms of compartmentalization exist, with the most relevant to prokaryotes being encapsulation via self-assembling protein-based compartments. One widespread example of such is that of encapsulins-cage-like protein nanocompartments able to compartmentalize specific reactions, pathways, and processes in bacteria and archaea. While still relatively nascent bioengineering tools, encapsulins exhibit many promising characteristics, including a number of defined compartment sizes ranging from 24 to 42 nm, straightforward expression, the ability to self-assemble via the Hong Kong 97-like fold, marked physical robustness, and internal and external handles primed for rational genetic and molecular manipulation. Moreover, encapsulins allow for facile and specific encapsulation of native or heterologous cargo proteins via naturally or rationally fused targeting peptide sequences. Taken together, the attributes of encapsulins promise substantial customizability and broad usability. This review discusses recent advances in employing engineered encapsulins across various fields, from their use as bionanoreactors to targeted delivery systems and beyond. A special focus will be provided on the rational engineering of encapsulin systems and their potential promise as biomolecular research tools.
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Affiliation(s)
- Jesse A Jones
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Tobias W Giessen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
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82
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Lončar N, Rozeboom HJ, Franken LE, Stuart MC, Fraaije MW. Structure of a robust bacterial protein cage and its application as a versatile biocatalytic platform through enzyme encapsulation. Biochem Biophys Res Commun 2020; 529:548-553. [DOI: 10.1016/j.bbrc.2020.06.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 01/15/2023]
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83
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Greening C, Lithgow T. Formation and function of bacterial organelles. Nat Rev Microbiol 2020; 18:677-689. [PMID: 32710089 DOI: 10.1038/s41579-020-0413-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2020] [Indexed: 01/28/2023]
Abstract
Advances in imaging technologies have revealed that many bacteria possess organelles with a proteomically defined lumen and a macromolecular boundary. Some are bound by a lipid bilayer (such as thylakoids, magnetosomes and anammoxosomes), whereas others are defined by a lipid monolayer (such as lipid bodies), a proteinaceous coat (such as carboxysomes) or have a phase-defined boundary (such as nucleolus-like compartments). These diverse organelles have various metabolic and physiological functions, facilitating adaptation to different environments and driving the evolution of cellular complexity. This Review highlights that, despite the diversity of reported organelles, some unifying concepts underlie their formation, structure and function. Bacteria have fundamental mechanisms of organelle formation, through which conserved processes can form distinct organelles in different species depending on the proteins recruited to the luminal space and the boundary of the organelle. These complex subcellular compartments provide evolutionary advantages as well as enabling metabolic specialization, biogeochemical processes and biotechnological advances. Growing evidence suggests that the presence of organelles is the rule, rather than the exception, in bacterial cells.
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Affiliation(s)
- Chris Greening
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.
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84
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Gabashvili AN, Chmelyuk NS, Efremova MV, Malinovskaya JA, Semkina AS, Abakumov MA. Encapsulins-Bacterial Protein Nanocompartments: Structure, Properties, and Application. Biomolecules 2020; 10:biom10060966. [PMID: 32604934 PMCID: PMC7355545 DOI: 10.3390/biom10060966] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/21/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
Recently, a new class of prokaryotic compartments, collectively called encapsulins or protein nanocompartments, has been discovered. The shell proteins of these structures self-organize to form icosahedral compartments with a diameter of 25-42 nm, while one or more cargo proteins with various functions can be encapsulated in the nanocompartment. Non-native cargo proteins can be loaded into nanocompartments and the surface of the shells can be further functionalized, which allows for developing targeted drug delivery systems or using encapsulins as contrast agents for magnetic resonance imaging. Since the genes encoding encapsulins can be integrated into the cell genome, encapsulins are attractive for investigation in various scientific fields, including biomedicine and nanotechnology.
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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.); (N.S.C.)
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova st, 1, 117997 Moscow, Russia;
| | - Nelly S. Chmelyuk
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (N.S.C.)
| | - Maria V. Efremova
- Department of Nuclear Medicine, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany;
- Institute of Biological and Medical Imaging and Institute of Developmental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | | | - Alevtina S. Semkina
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova st, 1, 117997 Moscow, Russia;
| | - Maxim A. Abakumov
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, Leninskiy Prospect, 4, 119049 Moscow, Russia; (A.N.G.); (N.S.C.)
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova st, 1, 117997 Moscow, Russia;
- Correspondence: ; Tel.: +7-903-586-4777
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85
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Bisanz JE, Soto-Perez P, Noecker C, Aksenov AA, Lam KN, Kenney GE, Bess EN, Haiser HJ, Kyaw TS, Yu FB, Rekdal VM, Ha CWY, Devkota S, Balskus EP, Dorrestein PC, Allen-Vercoe E, Turnbaugh PJ. A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria. Cell Host Microbe 2020; 27:1001-1013.e9. [PMID: 32348781 PMCID: PMC7292766 DOI: 10.1016/j.chom.2020.04.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/20/2020] [Accepted: 04/03/2020] [Indexed: 01/08/2023]
Abstract
Despite the remarkable microbial diversity found within humans, our ability to link genes to phenotypes is based upon a handful of model microorganisms. We report a comparative genomics platform for Eggerthella lenta and other Coriobacteriia, a neglected taxon broadly relevant to human health and disease. We uncover extensive genetic and metabolic diversity and validate a tool for mapping phenotypes to genes and sequence variants. We also present a tool for the quantification of strains from metagenomic sequencing data, enabling the identification of genes that predict bacterial fitness. Competitive growth is reproducible under laboratory conditions and attributable to intrinsic growth rates and resource utilization. Unique signatures of in vivo competition in gnotobiotic mice include an adhesin enriched in poor colonizers. Together, these computational and experimental resources represent a strong foundation for the continued mechanistic dissection of the Coriobacteriia and a template that can be applied to study other genetically intractable taxa.
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Affiliation(s)
- Jordan E Bisanz
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Paola Soto-Perez
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Cecilia Noecker
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Department of Pediatrics, Center for Microbiome Innovation, Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, CA 92093, USA
| | - Kathy N Lam
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Grace E Kenney
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Elizabeth N Bess
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Henry J Haiser
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Than S Kyaw
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Vayu M Rekdal
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Connie W Y Ha
- Department of Medicine, Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Suzanne Devkota
- Department of Medicine, Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Department of Pediatrics, Center for Microbiome Innovation, Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, CA 92093, USA
| | - Emma Allen-Vercoe
- Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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86
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Steinmetz NF, Lim S, Sainsbury F. Protein cages and virus-like particles: from fundamental insight to biomimetic therapeutics. Biomater Sci 2020; 8:2771-2777. [PMID: 32352101 PMCID: PMC8085892 DOI: 10.1039/d0bm00159g] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein cages (viral and non-viral) found in nature have evolved for a variety of purposes and are found in all kingdoms of life. The main functions of these nanoscale compartments are the protection and delivery of nucleic acids e.g. virus capsids, or the enrichment and sequestration of metabolons e.g. bacterial microcompartments. This review focuses on recent developments of protein cages for use in immunotherapy and therapeutic delivery. In doing so, we highlight the unique ways in which protein cages have informed on fundamental principles governing bio-nano interactions. With the enormous existing design space among naturally occurring protein cages, there is still much to learn from studying them as biomimetic particles.
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Affiliation(s)
- Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, CA 92093, USA and Department of Bioengineering, University of California, San Diego, CA 92093, USA and Department of Radiology, University of California, San Diego, CA 92093, USA and Moores Cancer Center, University of California, San Diego, CA 92093, USA and Center for Nano-ImmunoEngineering, University of California, San Diego, CA 92093, USA
| | - Sierin Lim
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457, Singapore and NTU-Northwestern Institute for Nanomedicine, Nanyang Technological University, Singapore 637457, Singapore
| | - Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia. and Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD 4001, Australia
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87
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Xing CY, Fan YC, Chen X, Guo JS, Shen Y, Yan P, Fang F, Chen YP. A self-assembled nanocompartment in anammox bacteria for resisting intracelluar hydroxylamine stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137030. [PMID: 32062250 DOI: 10.1016/j.scitotenv.2020.137030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
Anammox bacteria play an important role in the global nitrogen cycle, but research on anammoxosome structure is still in its initial stages. In particular, the anammox bacteria genome contains nanocompartments gene loci. However, the function and structure of the nanocompartments in anammox bacteria is poorly understood. We apply genetic engineering to demonstrate the self-assembled nanocompartments of anammox bacteria. The encapsulin shell protein (cEnc) and cargo protein hydroxylamine oxidoreductase (HAO) can self-assemble to form regular nanocompartments (about 128 nm in diameter) in vitro. Cell growth curve tests show that nanocompartments help model bacteria resist hydroxylamine (NH2OH) stress. Batch test results and transcriptional data show that cEnc and HAO are highly expressed in response to the negative effects of NH2OH on anammox efficiency, predicting a potential role of nanocompartments in helping anammox bacteria resist NH2OH stress. These findings improve our understanding of the mechanisms by which anammox bacteria respond to harmful environmental metabolites.
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Affiliation(s)
- Chong-Yang Xing
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligence Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu-Chen Fan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Xuan Chen
- 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
| | - 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
| | - 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 Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligence Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
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88
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Kogay R, Neely TB, Birnbaum DP, Hankel CR, Shakya M, Zhaxybayeva O. Machine-Learning Classification Suggests That Many Alphaproteobacterial Prophages May Instead Be Gene Transfer Agents. Genome Biol Evol 2020; 11:2941-2953. [PMID: 31560374 PMCID: PMC6821227 DOI: 10.1093/gbe/evz206] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2019] [Indexed: 12/20/2022] Open
Abstract
Many of the sequenced bacterial and archaeal genomes encode regions of viral provenance. Yet, not all of these regions encode bona fide viruses. Gene transfer agents (GTAs) are thought to be former viruses that are now maintained in genomes of some bacteria and archaea and are hypothesized to enable exchange of DNA within bacterial populations. In Alphaproteobacteria, genes homologous to the "head-tail" gene cluster that encodes structural components of the Rhodobacter capsulatus GTA (RcGTA) are found in many taxa, even if they are only distantly related to Rhodobacter capsulatus. Yet, in most genomes available in GenBank RcGTA-like genes have annotations of typical viral proteins, and therefore are not easily distinguished from their viral homologs without additional analyses. Here, we report a "support vector machine" classifier that quickly and accurately distinguishes RcGTA-like genes from their viral homologs by capturing the differences in the amino acid composition of the encoded proteins. Our open-source classifier is implemented in Python and can be used to scan homologs of the RcGTA genes in newly sequenced genomes. The classifier can also be trained to identify other types of GTAs, or even to detect other elements of viral ancestry. Using the classifier trained on a manually curated set of homologous viruses and GTAs, we detected RcGTA-like "head-tail" gene clusters in 57.5% of the 1,423 examined alphaproteobacterial genomes. We also demonstrated that more than half of the in silico prophage predictions are instead likely to be GTAs, suggesting that in many alphaproteobacterial genomes the RcGTA-like elements remain unrecognized.
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Affiliation(s)
- Roman Kogay
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | - Taylor B Neely
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire.,Amazon.com Inc., Seattle, WA
| | - Daniel P Birnbaum
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire.,School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Camille R Hankel
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire.,Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA
| | - Migun Shakya
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire.,Department of Computer Science, Dartmouth College, Hanover, New Hampshire
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89
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Ross J, Lambert T, Piergentili C, He D, Waldron KJ, Mackay CL, Marles-Wright J, Clarke DJ. Mass spectrometry reveals the assembly pathway of encapsulated ferritins and highlights a dynamic ferroxidase interface. Chem Commun (Camb) 2020; 56:3417-3420. [PMID: 32090213 DOI: 10.1039/c9cc08130e] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Encapsulated ferritins (EncFtn) are a recently characterised member of the ferritin superfamily. EncFtn proteins are sequestered within encapsulin nanocompartments and form a unique biological iron storage system. Here, we use native mass spectrometry and hydrogen-deuterium exchange mass spectrometry to elucidate the metal-mediated assembly pathway of EncFtn.
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Affiliation(s)
- Jennifer Ross
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, Scotland, UK.
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90
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Wong JX, Ogura K, Chen S, Rehm BHA. Bioengineered Polyhydroxyalkanoates as Immobilized Enzyme Scaffolds for Industrial Applications. Front Bioeng Biotechnol 2020; 8:156. [PMID: 32195237 PMCID: PMC7064635 DOI: 10.3389/fbioe.2020.00156] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/14/2020] [Indexed: 12/11/2022] Open
Abstract
Enzymes function as biocatalysts and are extensively exploited in industrial applications. Immobilization of enzymes using support materials has been shown to improve enzyme properties, including stability and functionality in extreme conditions and recyclability in biocatalytic processing. This review focuses on the recent advances utilizing the design space of in vivo self-assembled polyhydroxyalkanoate (PHA) particles as biocatalyst immobilization scaffolds. Self-assembly of biologically active enzyme-coated PHA particles is a one-step in vivo production process, which avoids the costly and laborious in vitro chemical cross-linking of purified enzymes to separately produced support materials. The homogeneous orientation of enzymes densely coating PHA particles enhances the accessibility of catalytic sites, improving enzyme function. The PHA particle technology has been developed into a remarkable scaffolding platform for the design of cost-effective designer biocatalysts amenable toward robust industrial bioprocessing. In this review, the PHA particle technology will be compared to other biological supramolecular assembly-based technologies suitable for in vivo enzyme immobilization. Recent progress in the fabrication of biological particulate scaffolds using enzymes of industrial interest will be summarized. Additionally, we outline innovative approaches to overcome limitations of in vivo assembled PHA particles to enable fine-tuned immobilization of multiple enzymes to enhance performance in multi-step cascade reactions, such as those used in continuous flow bioprocessing.
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Affiliation(s)
- Jin Xiang Wong
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- MacDiarmid Institute of Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington, New Zealand
| | - Kampachiro Ogura
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Shuxiong Chen
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
| | - Bernd H. A. Rehm
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
- Menzies Health Institute Queensland (MHIQ), Griffith University, Gold Coast Campus, Southport, QLD, Australia
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91
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Tracey JC, Coronado M, Giessen TW, Lau MCY, Silver PA, Ward BB. The Discovery of Twenty-Eight New Encapsulin Sequences, Including Three in Anammox Bacteria. Sci Rep 2019; 9:20122. [PMID: 31882935 PMCID: PMC6934571 DOI: 10.1038/s41598-019-56533-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 12/12/2019] [Indexed: 12/22/2022] Open
Abstract
Many prokaryotes encode protein-based encapsulin nanocompartments, including anaerobic ammonium oxidizing (anammox) bacteria. This study expands the list of known anammox encapsulin systems from freshwater species to include the marine genus Scalindua. Two novel systems, identified in "Candidatus Scalindua rubra" and "Candidatus Scalindua sp. SCAELEC01 167" possess different architectures than previously studied freshwater anammox encapsulins. Characterization of the S. rubra encapsulin confirms that it can self-assemble to form compartments when heterologously expressed in Escherichia coli. BLASTp and HMMER searches of additional genomes and metagenomes spanning a range of environments returned 26 additional novel encapsulins, including a freshwater anammox encapsulin identified in "Candidatus Brocadia caroliniensis". Phylogenetic analysis comparing these 28 new encapsulin sequences and cargo to that of their closest known relatives shows that encapsulins cluster by cargo protein type and therefore likely evolved together. Lastly, prokaryotic encapsulins may be more common and diverse than previously thought. Through searching a small sample size of all public metagenomes and genomes, many new encapsulin systems were unearthed by this study. This suggests that many additional encapsulins likely remain to be discovered.
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Affiliation(s)
- John C Tracey
- Princeton University, Department of Geosciences, Guyot Hall, Princeton, NJ, 08544, USA.
| | - Maricela Coronado
- Princeton University, Department of Geosciences, Guyot Hall, Princeton, NJ, 08544, USA
| | - Tobias W Giessen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Harvard Medical School, Department of Systems Biology, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Maggie C Y Lau
- Princeton University, Department of Geosciences, Guyot Hall, Princeton, NJ, 08544, USA
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Pamela A Silver
- Harvard Medical School, Department of Systems Biology, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Bess B Ward
- Princeton University, Department of Geosciences, Guyot Hall, Princeton, NJ, 08544, USA
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92
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Peng MW, Yu XL, Guan Y, Liu P, Yan P, Fang F, Guo J, Chen YP. Underlying Promotion Mechanism of High Concentration of Silver Nanoparticles on Anammox Process. ACS NANO 2019; 13:14500-14510. [PMID: 31794189 DOI: 10.1021/acsnano.9b08263] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Silver nanoparticles (AgNPs) are largely discharged into sewers and mostly accumulated in the sediments and sludge. The toxicity of AgNPs to environmental microorganisms has attracted great attention. However, the effect of AgNPs on anaerobic ammonium-oxidizing (anammox) granules remains unknown. Here we present the underlying promotion mechanism of AgNPs on anammox granules from a morphological and molecular biology perspective. Our results demonstrate a positive effect of AgNPs on the proliferation of anammox bacteria. AgNPs resulted in a change in the three-dimensional structure of anammox granules and led to larger pore size and higher porosity. In addition, the diffusion capacity of the substrate and metal ions was enhanced. Furthermore, the expression of anammox-related enzymes, such as nitrite oxidoreductase (NirS), hydrazine dehydrogenase (Hdh), and hydrazine synthase (HZS), was upregulated. Therefore, the growth rate and the nitrogen removal performance of the anammox granules were improved. Our findings clarify the underlying mechanism of AgNPs on anammox granules and provide a promising method for the treatment of AgNPs-rich wastewater.
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Affiliation(s)
- Meng-Wen Peng
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE , Chongqing University , Chongqing 400045 , China
| | - Xiu-Ling Yu
- Zhejiang Provincial Key Laboratory of Agricultural Resource and Environment , Zhejiang University , Hangzhou 310058 , China
| | - Yong Guan
- National Synchrotron Radiation Laboratory , University of Science and Technology of China , Hefei 230026 , China
| | - Peng Liu
- School of Environmental Studies , China University of Geosciences , Wuhan 430074 , China
| | - Peng Yan
- 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
| | - Jinsong Guo
- 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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93
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Lee TH, Carpenter TS, D'haeseleer P, Savage DF, Yung MC. Encapsulin carrier proteins for enhanced expression of antimicrobial peptides. Biotechnol Bioeng 2019; 117:603-613. [PMID: 31709513 DOI: 10.1002/bit.27222] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
Antimicrobial peptides (AMPs) are regarded as attractive alternatives to conventional antibiotics, but their production in microbes remains challenging due to their inherent bactericidal nature. To address these limitations, we have developed a novel AMP fusion protein system based on an encapsulin nanocompartment protein and have demonstrated its utility in enhancing expression of HBCM2, an AMP with activity against Gram-negative bacteria. Here, HBCM2 was fused to the N-terminus of several Encapsulin monomer (Enc) variants engineered with multiple TEV protease recognition site insertions to facilitate proteolytic release of the fused HBCM2. Fusion of HBCM2 to the Enc variants, but not other common carrier proteins, enabled robust overexpression in Escherichia coli C43(DE3) cells. Interestingly, variants with a TEV site insertion following residue K71 in Enc exhibited the highest overexpression and HBCM2 release efficiencies compared to other variants but were deficient in cage formation. HBCM2 was purified from the highest expressing variant following TEV protease digestion and was found to be highly active in inhibiting E. coli growth (MIC = 5 μg/ml). Our study demonstrates the potential use of the Enc system to enhance expression of AMPs for biomanufacturing and therapeutic applications.
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Affiliation(s)
- Tek-Hyung Lee
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Livermore, California
| | - Timothy S Carpenter
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Livermore, California
| | - Patrik D'haeseleer
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Livermore, California
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, California
| | - Mimi C Yung
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Livermore, California
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94
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Li TL, Wang Z, You H, Ong Q, Varanasi VJ, Dong M, Lu B, Paşca SP, Cui B. Engineering a Genetically Encoded Magnetic Protein Crystal. NANO LETTERS 2019; 19:6955-6963. [PMID: 31552740 PMCID: PMC7265822 DOI: 10.1021/acs.nanolett.9b02266] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Magnetogenetics is a new field that leverages genetically encoded proteins and protein assemblies that are sensitive to magnetic fields to study and manipulate cell behavior. Theoretical studies show that many proposed magnetogenetic proteins do not contain enough iron to generate substantial magnetic forces. Here, we have engineered a genetically encoded ferritin-containing protein crystal that grows inside mammalian cells. Each of these crystals contains more than 10 million ferritin subunits and is capable of mineralizing substantial amounts of iron. When isolated from cells and loaded with iron in vitro, these crystals generate magnetic forces that are 9 orders of magnitude larger than the forces from the single ferritin cages used in previous studies. These protein crystals are attracted to an applied magnetic field and move toward magnets even when internalized into cells. While additional studies are needed to realize the full potential of magnetogenetics, these results demonstrate the feasibility of engineering protein assemblies for magnetic sensing.
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Affiliation(s)
- Thomas L. Li
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305, United States
| | - Zegao Wang
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus 8000, Denmark
| | - He You
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Qunxiang Ong
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Vamsi J. Varanasi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus 8000, Denmark
| | - Bai Lu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Sergiu P. Paşca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305, United States
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Corresponding Author: Phone: (650) 725-9573.
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95
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Viborg AH, Terrapon N, Lombard V, Michel G, Czjzek M, Henrissat B, Brumer H. A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16). J Biol Chem 2019; 294:15973-15986. [PMID: 31501245 PMCID: PMC6827312 DOI: 10.1074/jbc.ra119.010619] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/05/2019] [Indexed: 12/12/2022] Open
Abstract
Glycoside hydrolase family (GH) 16 comprises a large and taxonomically diverse family of glycosidases and transglycosidases that adopt a common β-jelly-roll fold and are active on a range of terrestrial and marine polysaccharides. Presently, broadly insightful sequence–function correlations in GH16 are hindered by a lack of a systematic subfamily structure. To fill this gap, we have used a highly scalable protein sequence similarity network analysis to delineate nearly 23,000 GH16 sequences into 23 robust subfamilies, which are strongly supported by hidden Markov model and maximum likelihood molecular phylogenetic analyses. Subsequent evaluation of over 40 experimental three-dimensional structures has highlighted key tertiary structural differences, predominantly manifested in active-site loops, that dictate substrate specificity across the GH16 evolutionary landscape. As for other large GH families (i.e. GH5, GH13, and GH43), this new subfamily classification provides a roadmap for functional glycogenomics that will guide future bioinformatics and experimental structure–function analyses. The GH16 subfamily classification is publicly available in the CAZy database. The sequence similarity network workflow used here, SSNpipe, is freely available from GitHub.
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Affiliation(s)
- Alexander Holm Viborg
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France
| | - Gurvan Michel
- Sorbonne Universités, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Mirjam Czjzek
- Sorbonne Universités, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France .,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada .,Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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96
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Sigmund F, Pettinger S, Kube M, Schneider F, Schifferer M, Schneider S, Efremova MV, Pujol-Martí J, Aichler M, Walch A, Misgeld T, Dietz H, Westmeyer GG. Iron-Sequestering Nanocompartments as Multiplexed Electron Microscopy Gene Reporters. ACS NANO 2019; 13:8114-8123. [PMID: 31194509 DOI: 10.1021/acsnano.9b03140] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Multicolored gene reporters for light microscopy are indispensable for biomedical research, but equivalent genetic tools for electron microscopy (EM) are still rare despite the increasing importance of nanometer resolution for reverse engineering of molecular machinery and reliable mapping of cellular circuits. We here introduce the fully genetic encapsulin/cargo system of Quasibacillus thermotolerans (Qt), which in combination with the recently characterized encapsulin system from Myxococcus xanthus (Mx) enables multiplexed gene reporter imaging via conventional transmission electron microscopy (TEM) in mammalian cells. Cryo-electron reconstructions revealed that the Qt encapsulin shell self-assembles to nanospheres with T = 4 icosahedral symmetry and a diameter of ∼43 nm harboring two putative pore regions at the 5-fold and 3-fold axes. We also found that upon heterologous expression in mammalian cells, the native cargo is autotargeted to the inner surface of the shell and exhibits ferroxidase activity leading to efficient intraluminal iron biomineralization, which enhances cellular TEM contrast. We furthermore demonstrate that the two differently sized encapsulins of Qt and Mx do not intermix and can be robustly differentiated by conventional TEM via a deep learning classifier to enable automated multiplexed EM gene reporter imaging.
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Affiliation(s)
- Felix Sigmund
- Department of Nuclear Medicine, TUM School of Medicine , Technical University of Munich , 81675 Munich , Germany
- Institute of Biological and Medical Imaging , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Institute of Developmental Genetics , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Susanne Pettinger
- Department of Nuclear Medicine, TUM School of Medicine , Technical University of Munich , 81675 Munich , Germany
- Institute of Biological and Medical Imaging , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Institute of Developmental Genetics , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Massimo Kube
- Laboratory for Biomolecular Design, Department of Physics , Technical University of Munich , 85748 Garching , Germany
| | - Fabian Schneider
- Laboratory for Biomolecular Design, Department of Physics , Technical University of Munich , 85748 Garching , Germany
| | - Martina Schifferer
- Institute of Neuronal Cell Biology, TUM School of Medicine , Technical University of Munich , 80802 Munich , Germany
- German Center for Neurodegenerative Diseases (DZNE) , 81377 Munich , Germany
| | - Steffen Schneider
- Computational Neuroengineering, Department of Electrical and Computer Engineering , Technical University of Munich , 80333 Munich , Germany
- Tübingen AI Center , University of Tübingen , 72076 Tübingen , Germany
| | - Maria V Efremova
- Department of Nuclear Medicine, TUM School of Medicine , Technical University of Munich , 81675 Munich , Germany
- Institute of Biological and Medical Imaging , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Institute of Developmental Genetics , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Laboratory of Chemical Design of Bionanomaterials for Medical Applications, Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russian Federation
| | - Jesús Pujol-Martí
- Department "Circuits - Computation - Models" , Max Planck Institute of Neurobiology , 82152 Martinsried , Germany
| | - Michaela Aichler
- Research Unit Analytical Pathology , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Axel Walch
- Research Unit Analytical Pathology , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Thomas Misgeld
- Institute of Neuronal Cell Biology, TUM School of Medicine , Technical University of Munich , 80802 Munich , Germany
- German Center for Neurodegenerative Diseases (DZNE) , 81377 Munich , Germany
| | - Hendrik Dietz
- Laboratory for Biomolecular Design, Department of Physics , Technical University of Munich , 85748 Garching , Germany
| | - Gil G Westmeyer
- Department of Nuclear Medicine, TUM School of Medicine , Technical University of Munich , 81675 Munich , Germany
- Institute of Biological and Medical Imaging , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Institute of Developmental Genetics , Helmholtz Zentrum München , 85764 Neuherberg , Germany
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97
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Giessen TW, Orlando BJ, Verdegaal AA, Chambers MG, Gardener J, Bell DC, Birrane G, Liao M, Silver PA. Large protein organelles form a new iron sequestration system with high storage capacity. eLife 2019; 8:46070. [PMID: 31282860 PMCID: PMC6668986 DOI: 10.7554/elife.46070] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/06/2019] [Indexed: 12/21/2022] Open
Abstract
Iron storage proteins are essential for cellular iron homeostasis and redox balance. Ferritin proteins are the major storage units for bioavailable forms of iron. Some organisms lack ferritins, and it is not known how they store iron. Encapsulins, a class of protein-based organelles, have recently been implicated in microbial iron and redox metabolism. Here, we report the structural and mechanistic characterization of a 42 nm two-component encapsulin-based iron storage compartment from Quasibacillus thermotolerans. Using cryo-electron microscopy and x-ray crystallography, we reveal the assembly principles of a thermostable T = 4 shell topology and its catalytic ferroxidase cargo and show interactions underlying cargo-shell co-assembly. This compartment has an exceptionally large iron storage capacity storing over 23,000 iron atoms. Our results reveal a new approach for survival in diverse habitats with limited or fluctuating iron availability via an iron storage system able to store 10 to 20 times more iron than ferritin. People often think of the cell as the basic unit of life. Despite this, individual cells are also subdivided into many compartments, called ‘organelles’ because they act like the internal organs of the cell. For example, organelles can break down nutrients, store information in the form of DNA, or help remove waste. Even bacterial cells, despite being smaller and simpler than most other cell types, contain organelle-like structures. These are tiny compartments, termed protein organelles, which are enclosed by ‘shells’ made from self-assembling proteins within the cell. Cells need iron to carry out the chemical reactions necessary for life. Iron is therefore an essential nutrient, but it can also be toxic if not stored properly inside the cell. Cells often solve this problem by locking iron away inside small, specialised protein cages called ferritins until it can be used. Most organisms, from humans to bacteria, have ferritins, but some do not, and the way these organisms store iron remains largely unknown. The bacterium Quasibacillus thermotolerans is an example of an organism that lacks ferritins. However, it does contain a recently discovered type of protein organelle, called an encapsulin. Giessen et al. wanted to find out more about the structure of this protein organelle, and to determine if it helped these bacteria store iron. Q. thermotolerans’ encapsulin turned out to be the largest of its kind discovered to date. Detailed imaging experiments, using a combination of electron microscopy and X-ray- based techniques, revealed that the protein shell of the encapsulin had an overall structure resembling chain mail and contained multiple pores. These pores were negatively charged, meaning that they could efficiently attract iron (which has a positive charge) and funnel it into the interior of the compartment. The compartment itself was able to store at least 20 times more iron than ferritins, making this encapsulin one of the most efficient methods of iron storage in any cell. These findings will help us better understand how bacteria that lack ferritins cope with the problem of iron storage. In the future, encapsulins could also be used as a target for new therapies to fight bacterial infections, or even as the building blocks for microscopic chemical reactors or ‘storage facilities’ in industrial applications.
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Affiliation(s)
- Tobias W Giessen
- Department of Systems Biology, Harvard Medical School, Boston, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, United States
| | - Benjamin J Orlando
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Andrew A Verdegaal
- Department of Systems Biology, Harvard Medical School, Boston, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States
| | - Melissa G Chambers
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Jules Gardener
- Center for Nanoscale Systems, Harvard University, Cambridge, United States
| | - David C Bell
- Center for Nanoscale Systems, Harvard University, Cambridge, United States.,School of Engineering and Applied Sciences, Harvard University, Cambridge, United States
| | - Gabriel Birrane
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, United States
| | - Maofu Liao
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, United States
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98
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Kim D, Choi J, Lee S, Hyun H, Lee K, Cho K. Mutants defective in the production of encapsulin show a tan-phase-locked phenotype in Myxococcus xanthus. J Microbiol 2019; 57:795-802. [PMID: 31187417 DOI: 10.1007/s12275-019-8683-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/06/2019] [Accepted: 04/08/2019] [Indexed: 10/26/2022]
Abstract
Myxococcus xanthus, a myxobacterium, displays phase variation between yellow phase and tan phase. We found that deletion of the encA gene encoding encapsulin and the encF gene encoding a metalloprotease causes formation of tan colonies that never transform into yellow colonies. The encA and encF mutants were defective in the production of DK-xanthene and myxovirescin. They did not produce extracellular polysaccharides; hence, the cells did not aggregate in liquid and showed reduced swarming on agar plates. The mutants had defective sporulation, but were rescued extracellularly by wild type cells. All these traits indicate that the encA and encF mutants are likely to be tan-phase-locked, and encapsulin has a close relationship with phase variation in M. xanthus. The encA and encF genes are localized in the same gene cluster, encBAEFG (MXAN_3557~MXAN_3553). Unlike the encA and encF genes, deletion of other genes in the cluster did not show tan-phase-locked phenotype.
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Affiliation(s)
- Dohee Kim
- Department of Biotechnology, Hoseo University, Asan, 31499, Republic of Korea
| | - Juo Choi
- Department of Biotechnology, Hoseo University, Asan, 31499, Republic of Korea
| | - Sunjin Lee
- Department of Biotechnology, Hoseo University, Asan, 31499, Republic of Korea
| | - Hyesook Hyun
- Department of Biotechnology, Hoseo University, Asan, 31499, Republic of Korea
| | - Kyoung Lee
- Department of Microbiology, Changwon National University, Changwon, 51140, Republic of Korea
| | - Kyungyun Cho
- Department of Biotechnology, Hoseo University, Asan, 31499, Republic of Korea.
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99
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Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea. Biochem J 2019; 476:975-989. [PMID: 30837306 DOI: 10.1042/bcj20180922] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 11/17/2022]
Abstract
Ferritins are a large family of intracellular proteins that protect the cell from oxidative stress by catalytically converting Fe(II) into less toxic Fe(III) and storing iron minerals within their core. Encapsulated ferritins (EncFtn) are a sub-family of ferritin-like proteins, which are widely distributed in all bacterial and archaeal phyla. The recently characterized Rhodospirillum rubrum EncFtn displays an unusual structure when compared with classical ferritins, with an open decameric structure that is enzymatically active, but unable to store iron. This EncFtn must be associated with an encapsulin nanocage in order to act as an iron store. Given the wide distribution of the EncFtn family in organisms with diverse environmental niches, a question arises as to whether this unusual structure is conserved across the family. Here, we characterize EncFtn proteins from the halophile Haliangium ochraceum and the thermophile Pyrococcus furiosus, which show the conserved annular pentamer of dimers topology. Key structural differences are apparent between the homologues, particularly in the centre of the ring and the secondary metal-binding site, which is not conserved across the homologues. Solution and native mass spectrometry analyses highlight that the stability of the protein quaternary structure differs between EncFtn proteins from different species. The ferroxidase activity of EncFtn proteins was confirmed, and we show that while the quaternary structure around the ferroxidase centre is distinct from classical ferritins, the ferroxidase activity is still inhibited by Zn(II). Our results highlight the common structural organization and activity of EncFtn proteins, despite diverse host environments and contexts within encapsulins.
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100
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de Ruiter MV, Klem R, Luque D, Cornelissen JJLM, Castón JR. Structural nanotechnology: three-dimensional cryo-EM and its use in the development of nanoplatforms for in vitro catalysis. NANOSCALE 2019; 11:4130-4146. [PMID: 30793729 DOI: 10.1039/c8nr09204d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The organization of enzymes into different subcellular compartments is essential for correct cell function. Protein-based cages are a relatively recently discovered subclass of structurally dynamic cellular compartments that can be mimicked in the laboratory to encapsulate enzymes. These synthetic structures can then be used to improve our understanding of natural protein-based cages, or as nanoreactors in industrial catalysis, metabolic engineering, and medicine. Since the function of natural protein-based cages is related to their three-dimensional structure, it is important to determine this at the highest possible resolution if viable nanoreactors are to be engineered. Cryo-electron microscopy (cryo-EM) is ideal for undertaking such analyses within a feasible time frame and at near-native conditions. This review describes how three-dimensional cryo-EM is used in this field and discusses its advantages. An overview is also given of the nanoreactors produced so far, their structure, function, and applications.
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Affiliation(s)
- Mark V de Ruiter
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands.
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