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Andreas MP, Giessen TW. The biosynthesis of the odorant 2-methylisoborneol is compartmentalized inside a protein shell. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590730. [PMID: 38712110 PMCID: PMC11071394 DOI: 10.1101/2024.04.23.590730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Terpenoids are the largest class of natural products, found across all domains of life. One of the most abundant bacterial terpenoids is the volatile odorant 2-methylisoborneol (2-MIB), partially responsible for the earthy smell of soil and musty taste of contaminated water. Many bacterial 2-MIB biosynthetic gene clusters were thought to encode a conserved transcription factor, named EshA in the model soil bacterium Streptomyces griseus . Here, we revise the function of EshA, now referred to as Sg Enc, and show that it is a Family 2B encapsulin shell protein. Using cryo-electron microscopy, we find that Sg Enc forms an icosahedral protein shell and encapsulates 2-methylisoborneol synthase (2-MIBS) as a cargo protein. Sg Enc contains a cyclic adenosine monophosphate (cAMP) binding domain (CBD)-fold insertion and a unique metal-binding domain, both displayed on the shell exterior. We show that Sg Enc CBDs do not bind cAMP. We find that 2-MIBS cargo loading is mediated by an N-terminal disordered cargo-loading domain and that 2-MIBS activity and Sg Enc shell structure are not modulated by cAMP. Our work redefines the function of EshA and establishes Family 2B encapsulins as cargo-loaded protein nanocompartments involved in secondary metabolite biosynthesis.
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2
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Abstract
Subcellular compartmentalization is a defining feature of all cells. In prokaryotes, compartmentalization is generally achieved via protein-based strategies. The two main classes of microbial protein compartments are bacterial microcompartments and encapsulin nanocompartments. Encapsulins self-assemble into proteinaceous shells with diameters between 24 and 42 nm and are defined by the viral HK97-fold of their shell protein. Encapsulins have the ability to encapsulate dedicated cargo proteins, including ferritin-like proteins, peroxidases, and desulfurases. Encapsulation is mediated by targeting sequences present in all cargo proteins. Encapsulins are found in many bacterial and archaeal phyla and have been suggested to play roles in iron storage, stress resistance, sulfur metabolism, and natural product biosynthesis. Phylogenetic analyses indicate that they share a common ancestor with viral capsid proteins. Many pathogens encode encapsulins, and recent evidence suggests that they may contribute toward pathogenicity. The existing information on encapsulin structure, biochemistry, biological function, and biomedical relevance is reviewed here.
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Affiliation(s)
- Tobias W. Giessen
- Departments of Biomedical Engineering and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
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3
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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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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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5
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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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6
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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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7
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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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8
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Nichols RJ, Cassidy-Amstutz C, Chaijarasphong T, Savage DF. Encapsulins: molecular biology of the shell. Crit Rev Biochem Mol Biol 2017. [DOI: 10.1080/10409238.2017.1337709] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Robert J. Nichols
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA, USA
| | | | | | - David F. Savage
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA, USA
- Department of Chemistry, UC Berkeley, Berkeley, CA, USA
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9
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Abstract
Viruses are the most abundant biological entities on earth and show remarkable diversity of genome sequences, replication and expression strategies, and virion structures. Evolutionary genomics of viruses revealed many unexpected connections but the general scenario(s) for the evolution of the virosphere remains a matter of intense debate among proponents of the cellular regression, escaped genes, and primordial virus world hypotheses. A comprehensive sequence and structure analysis of major virion proteins indicates that they evolved on about 20 independent occasions, and in some of these cases likely ancestors are identifiable among the proteins of cellular organisms. Virus genomes typically consist of distinct structural and replication modules that recombine frequently and can have different evolutionary trajectories. The present analysis suggests that, although the replication modules of at least some classes of viruses might descend from primordial selfish genetic elements, bona fide viruses evolved on multiple, independent occasions throughout the course of evolution by the recruitment of diverse host proteins that became major virion components.
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10
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Giessen TW. Encapsulins: microbial nanocompartments with applications in biomedicine, nanobiotechnology and materials science. Curr Opin Chem Biol 2016; 34:1-10. [PMID: 27232770 DOI: 10.1016/j.cbpa.2016.05.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 11/17/2022]
Abstract
Compartmentalization is one of the defining features of life. Cells use protein compartments to exert spatial control over their metabolism, store nutrients and create unique microenvironments needed for essential physiological processes. Encapsulins are a recently discovered class of protein nanocompartments found in bacteria and archaea that naturally encapsulate cargo proteins. A short C-terminal targeting sequence directs the highly specific encapsulation process in vivo. Here, I will initially discuss the properties, diversity and putative function of encapsulins. The unique characteristics and potential uses of the self-sorting cargo-packaging process found in encapsulin systems will then be highlighted. Examples for the application of encapsulins as cell-specific optical nanoprobes and targeted therapeutic delivery systems will be discussed with an emphasis on the ability to integrate multiple functionalities within a single nanodevice. By fusing targeting sequences to non-native proteins, encapsulins can also be used as specific nanocontainers and enzymatic nanoreactors in vivo. I will end by briefly discussing future avenues for encapsulin research related to both basic microbial metabolism and applications in biomedicine, catalysis and materials science.
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Affiliation(s)
- Tobias W Giessen
- Department of Systems Biology, Harvard Medical School and Wyss Institute for Biologically Inspired Engineering, Harvard University, 200 Longwood Ave, Boston, MA 02115, USA.
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11
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Abstract
First discovered in bacteriophage HK97, biological chainmail is a highly stable system formed by concatenated protein rings. Each subunit of the ring contains the HK97-like fold, which is characterized by its submarine-like shape with a 5-stranded β sheet in the axial (A) domain, spine helix in the peripheral (P) domain, and an extended (E) loop. HK97 capsid consists of covalently-linked copies of just one HK97-like fold protein and represents the most effective strategy to form highly stable chainmail needed for dsDNA genome encapsidation. Recently, near-atomic resolution structures enabled by cryo electron microscopy (cryoEM) have revealed a range of other, more complex variants of this strategy for constructing dsDNA viruses. The first strategy, exemplified by P22-like phages, is the attachment of an insertional (I) domain to the core 5-stranded β sheet of the HK97-like fold. The atomic models of the Bordetella phage BPP-1 showcases an alternative topology of the classic HK97 topology of the HK97-like fold, as well as the second strategy for constructing stable capsids, where an auxiliary jellyroll protein dimer serves to cement the non-covalent chainmail formed by capsid protein subunits. The third strategy, found in lambda-like phages, uses auxiliary protein trimers to stabilize the underlying non-covalent chainmail near the 3-fold axis. Herpesviruses represent highly complex viruses that use a combination of these strategies, resulting in four-level hierarchical organization including a non-covalent chainmail formed by the HK97-like fold domain found in the floor region. A thorough understanding of these structures should help unlock the enigma of the emergence and evolution of dsDNA viruses and inform bioengineering efforts based on these viruses.
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Affiliation(s)
- Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA.,California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
| | - Joshua Chiou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
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12
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Suhanovsky MM, Teschke CM. Nature's favorite building block: Deciphering folding and capsid assembly of proteins with the HK97-fold. Virology 2015; 479-480:487-97. [PMID: 25864106 PMCID: PMC4424165 DOI: 10.1016/j.virol.2015.02.055] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/24/2015] [Accepted: 02/27/2015] [Indexed: 01/08/2023]
Abstract
For many (if not all) bacterial and archaeal tailed viruses and eukaryotic Herpesvirdae the HK97-fold serves as the major architectural element in icosahedral capsid formation while still enabling the conformational flexibility required during assembly and maturation. Auxiliary proteins or Δ-domains strictly control assembly of multiple, identical, HK97-like subunits into procapsids with specific icosahedral symmetries, rather than aberrant non-icosahedral structures. Procapsids are precursor structures that mature into capsids in a process involving release of auxiliary proteins (or cleavage of Δ-domains), dsDNA packaging, and conformational rearrangement of the HK97-like subunits. Some coat proteins built on the ubiquitous HK97-fold also have accessory domains or loops that impart specific functions, such as increased monomer, procapsid, or capsid stability. In this review, we analyze the numerous HK97-like coat protein structures that are emerging in the literature (over 40 at time of writing) by comparing their topology, additional domains, and their assembly and misassembly reactions.
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Affiliation(s)
- Margaret M Suhanovsky
- Department of Molecular and Cell Biology, University of Connecticut, 91N. Eagleville Rd. Storrs, CT 06269-3125, USA.
| | - Carolyn M Teschke
- Department of Molecular and Cell Biology, University of Connecticut, 91N. Eagleville Rd. Storrs, CT 06269-3125, USA; Department of Chemistry, University of Connecticut, 91N. Eagleville Rd. Storrs, CT 06269-3125, USA.
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13
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Freire JM, Santos NC, Veiga AS, Da Poian AT, Castanho MARB. Rethinking the capsid proteins of enveloped viruses: multifunctionality from genome packaging to genome transfection. FEBS J 2015; 282:2267-78. [DOI: 10.1111/febs.13274] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/05/2015] [Accepted: 03/17/2015] [Indexed: 11/29/2022]
Affiliation(s)
- João M. Freire
- Instituto de Medicina Molecular; Faculdade de Medicina; Universidade de Lisboa; Lisbon Portugal
| | - Nuno C. Santos
- Instituto de Medicina Molecular; Faculdade de Medicina; Universidade de Lisboa; Lisbon Portugal
| | - Ana Salomé Veiga
- Instituto de Medicina Molecular; Faculdade de Medicina; Universidade de Lisboa; Lisbon Portugal
| | - Andrea T. Da Poian
- Instituto de Bioquímica Médica Leopoldo de Meis; Universidade Federal do Rio de Janeiro; Rio de Janeiro Brazil
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14
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Tamura A, Fukutani Y, Takami T, Fujii M, Nakaguchi Y, Murakami Y, Noguchi K, Yohda M, Odaka M. Packaging guest proteins into the encapsulin nanocompartment fromRhodococcus erythropolisN771. Biotechnol Bioeng 2014; 112:13-20. [DOI: 10.1002/bit.25322] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/16/2014] [Accepted: 06/25/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Akio Tamura
- Department of Biotechnology and Life Science; Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Yosuke Fukutani
- Department of Biotechnology and Life Science; Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Taku Takami
- Department of Organic Polymer Material Chemistry; Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Motoko Fujii
- Department of Biotechnology and Life Science; Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Yuki Nakaguchi
- Department of Biotechnology and Life Science; Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Yoshihiko Murakami
- Department of Organic Polymer Material Chemistry; Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Keiichi Noguchi
- Instrumentation Analysis Center; Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science; Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Masafumi Odaka
- Department of Biotechnology and Life Science; Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
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15
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McHugh CA, Fontana J, Nemecek D, Cheng N, Aksyuk AA, Heymann JB, Winkler DC, Lam AS, Wall JS, Steven AC, Hoiczyk E. A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress. EMBO J 2014; 33:1896-911. [PMID: 25024436 DOI: 10.15252/embj.201488566] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Living cells compartmentalize materials and enzymatic reactions to increase metabolic efficiency. While eukaryotes use membrane-bound organelles, bacteria and archaea rely primarily on protein-bound nanocompartments. Encapsulins constitute a class of nanocompartments widespread in bacteria and archaea whose functions have hitherto been unclear. Here, we characterize the encapsulin nanocompartment from Myxococcus xanthus, which consists of a shell protein (EncA, 32.5 kDa) and three internal proteins (EncB, 17 kDa; EncC, 13 kDa; EncD, 11 kDa). Using cryo-electron microscopy, we determined that EncA self-assembles into an icosahedral shell 32 nm in diameter (26 nm internal diameter), built from 180 subunits with the fold first observed in bacteriophage HK97 capsid. The internal proteins, of which EncB and EncC have ferritin-like domains, attach to its inner surface. Native nanocompartments have dense iron-rich cores. Functionally, they resemble ferritins, cage-like iron storage proteins, but with a massively greater capacity (~30,000 iron atoms versus ~3,000 in ferritin). Physiological data reveal that few nanocompartments are assembled during vegetative growth, but they increase fivefold upon starvation, protecting cells from oxidative stress through iron sequestration.
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Affiliation(s)
- Colleen A McHugh
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Juan Fontana
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Daniel Nemecek
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Anastasia A Aksyuk
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - J Bernard Heymann
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Dennis C Winkler
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Alan S Lam
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Joseph S Wall
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Egbert Hoiczyk
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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16
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Heinemann J, Hamerly T, Maaty WS, Movahed N, Steffens JD, Reeves BD, Hilmer JK, Therien J, Grieco PA, Peters JW, Bothner B. Expanding the paradigm of thiol redox in the thermophilic root of life. Biochim Biophys Acta Gen Subj 2013; 1840:80-5. [PMID: 23962628 DOI: 10.1016/j.bbagen.2013.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/07/2013] [Accepted: 08/11/2013] [Indexed: 11/30/2022]
Abstract
BACKGROUND The current paradigm of intracellular redox chemistry maintains that cells establish a reducing environment maintained by a pool of small molecule and protein thiol to protect against oxidative damage. This strategy is conserved in mesophilic organisms from all domains of life, but has been confounded in thermophilic organisms where evidence suggests that intracellular proteins have abundant disulfides. METHODS Chemical labeling and 2-dimensional gel electrophoresis were used to capture disulfide bonding in the proteome of the model thermophile Sulfolobus solfataricus. The redox poise of the metabolome was characterized using both chemical labeling and untargeted liquid chromatography mass spectrometry. Gene annotation was undertaken using support vector machine based pattern recognition. RESULTS Proteomic analysis indicated the intracellular protein thiol of S. solfataricus was primarily in the disulfide form. Metabolic characterization revealed a lack of reduced small molecule thiol. Glutathione was found primarily in the oxidized state (GSSG), at relatively low concentration. Combined with genetic analysis, this evidence shows that pathways for synthesis of glutathione do exist in the archaeal domain. CONCLUSIONS In observed thermophilic organisms, thiol abundance and redox poise suggest that this system is not directly utilized for protection against oxidative damage. Instead, a more oxidized intracellular environment promotes disulfide bonding, a critical adaptation for protein thermostability. GENERAL SIGNIFICANCE Based on the placement of thermophilic archaea close to the last universal common ancestor in rRNA phylogenies, we hypothesize that thiol-based redox systems are derived from metabolic pathways originally tasked with promoting protein stability.
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Affiliation(s)
- Joshua Heinemann
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
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17
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Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story. Proc Natl Acad Sci U S A 2013; 110:10604-9. [PMID: 23733949 DOI: 10.1073/pnas.1303047110] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has been proposed that viruses can be divided into a small number of structure-based viral lineages. One of these lineages is exemplified by bacterial virus Hong Kong 97 (HK97), which represents the head-tailed dsDNA bacteriophages. Seemingly similar viruses also infect archaea. Here we demonstrate using genomic analysis, electron cryomicroscopy, and image reconstruction that the major coat protein fold of newly isolated archaeal Haloarcula sinaiiensis tailed virus 1 has the canonical coat protein fold of HK97. Although it has been anticipated previously, this is physical evidence that bacterial and archaeal head-tailed viruses share a common architectural principle. The HK97-like fold has previously been recognized also in herpesviruses, and this study expands the HK97-like lineage to viruses from all three domains of life. This is only the second established lineage to include archaeal, bacterial, and eukaryotic viruses. Thus, our findings support the hypothesis that the last common universal ancestor of cellular organisms was infected by a number of different viruses.
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18
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Senčilo A, Jacobs-Sera D, Russell DA, Ko CC, Bowman CA, Atanasova NS, Österlund E, Oksanen HM, Bamford DH, Hatfull GF, Roine E, Hendrix RW. Snapshot of haloarchaeal tailed virus genomes. RNA Biol 2013; 10:803-16. [PMID: 23470522 DOI: 10.4161/rna.24045] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The complete genome sequences of archaeal tailed viruses are currently highly underrepresented in sequence databases. Here, we report the genomic sequences of 10 new tailed viruses infecting different haloarchaeal hosts. Among these, only two viral genomes are closely related to each other and to previously described haloviruses HF1 and HF2. The approximately 760 kb of new genomic sequences in total shows no matches to CRISPR/Cas spacer sequences in haloarchaeal host genomes. Despite their high divergence, we were able to identify virion structural and assembly genes as well as genes coding for DNA and RNA metabolic functions. Interestingly, we identified many genes and genomic features that are shared with tailed bacteriophages, consistent with the hypothesis that haloarchaeal and bacterial tailed viruses share common ancestry, and that a viral lineage containing archaeal viruses, bacteriophages and eukaryotic viruses predates the division of the three major domains of non-viral life. However, as in tailed viruses in general and in haloarchaeal tailed viruses in particular, there are still a considerable number of predicted genes of unknown function.
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Affiliation(s)
- Ana Senčilo
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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19
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Veesler D, Quispe J, Grigorieff N, Potter CS, Carragher B, Johnson JE. Maturation in action: CryoEM study of a viral capsid caught during expansion. Structure 2012; 20:1384-90. [PMID: 22748764 DOI: 10.1016/j.str.2012.05.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Revised: 05/20/2012] [Accepted: 05/21/2012] [Indexed: 10/28/2022]
Abstract
Bacteriophage HK97 maturation involves discrete intermediate particle forms, comparable to transitional states in protein folding, before reaching its mature form. The process starts by formation of a metastable prohead, poised for exothermic expansion triggered by DNA packaging. During maturation, the capsid subunit transitions from a strained to a canonical tertiary conformation and this has been postulated to be the driving mechanism for initiating expansion via switching hexameric capsomer architecture from skewed to 6-fold symmetric. We report the subnanometer electron-cryomicroscopy reconstruction of the HK97 first expansion intermediate before any crosslink formation. This form displays 6-fold symmetric hexamers, but capsid subunit tertiary structures exhibit distortions comparable to the prohead forms. We propose that coat subunit strain release acts in synergy with the first crosslinks to drive forward maturation. Finally, we speculate that the energetic features of this transition may result from increased stability of intermediates during maturation via enhanced inter-subunit interactions.
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Affiliation(s)
- David Veesler
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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20
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Abstract
We examine virus maturation of selected nonenveloped and enveloped single-stranded RNA viruses, retroviruses, bacteriophages, and herpesviruses. Processes associated with maturation in the RNA viruses range from subtle (nodaviruses and picornaviruses) to dramatic (tetraviruses and togaviruses). The elaborate assembly and maturation pathway of HIV is discussed in contrast to the less sophisticated but highly efficient processes associated with togaviruses. Bacteriophage assembly and maturation are discussed in general terms, with specific examples chosen for emphasis. Finally the herpesviruses are compared with bacteriophages. The data support divergent evolution of nodaviruses, picornaviruses, and tetraviruses from a common ancestor and divergent evolution of alphaviruses and flaviviruses from a common ancestor. Likewise, bacteriophages and herpesviruses almost certainly share a common ancestor in their evolution. Comparing all the viruses, we conclude that maturation is a convergent process that is required to solve conflicting requirements in biological dynamics and function.
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Affiliation(s)
- David Veesler
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
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21
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Mokili JL, Rohwer F, Dutilh BE. Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2012; 2:63-77. [PMID: 22440968 PMCID: PMC7102772 DOI: 10.1016/j.coviro.2011.12.004] [Citation(s) in RCA: 386] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 12/09/2011] [Accepted: 12/12/2011] [Indexed: 01/21/2023]
Abstract
Monitoring the emergence and re-emergence of viral diseases with the goal of containing the spread of viral agents requires both adequate preparedness and quick response. Identifying the causative agent of a new epidemic is one of the most important steps for effective response to disease outbreaks. Traditionally, virus discovery required propagation of the virus in cell culture, a proven technique responsible for the identification of the vast majority of viruses known to date. However, many viruses cannot be easily propagated in cell culture, thus limiting our knowledge of viruses. Viral metagenomic analyses of environmental samples suggest that the field of virology has explored less than 1% of the extant viral diversity. In the last decade, the culture-independent and sequence-independent metagenomic approach has permitted the discovery of many viruses in a wide range of samples. Phylogenetically, some of these viruses are distantly related to previously discovered viruses. In addition, 60-99% of the sequences generated in different viral metagenomic studies are not homologous to known viruses. In this review, we discuss the advances in the area of viral metagenomics during the last decade and their relevance to virus discovery, clinical microbiology and public health. We discuss the potential of metagenomics for characterization of the normal viral population in a healthy community and identification of viruses that could pose a threat to humans through zoonosis. In addition, we propose a new model of the Koch's postulates named the 'Metagenomic Koch's Postulates'. Unlike the original Koch's postulates and the Molecular Koch's postulates as formulated by Falkow, the metagenomic Koch's postulates focus on the identification of metagenomic traits in disease cases. The metagenomic traits that can be traced after healthy individuals have been exposed to the source of the suspected pathogen.
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Affiliation(s)
- John L Mokili
- Department of Biology, San Diego State University, San Diego, CA 92182, USA.
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