1
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Oikeh E, Ziebarth J, Dinar MAM, Kirchhoff D, Aronova A, Dziubla TD, Wang Y, DeRouchey JE. DNA Packaging and Polycation Length Determine DNA Susceptibility to Free Radical Damage in Condensed DNA. J Phys Chem B 2024; 128:3329-3339. [PMID: 38557033 DOI: 10.1021/acs.jpcb.3c06116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In nature, DNA exists primarily in a highly compacted form. The compaction of DNA in vivo is mediated by cationic proteins: histones in somatic nuclei and protamines in sperm chromatin. The extreme, nearly crystalline packaging of DNA by protamines in spermatozoa is thought to be essential for both efficient genetic delivery as well as DNA protection against damage by mutagens and oxidative species. The protective role of protamines is required in sperm, as they are sensitive to ROS damage due to the progressive loss of DNA repair mechanisms during maturation. The degree to which DNA packaging directly relates to DNA protection in the condensed state, however, is poorly understood. Here, we utilized different polycation condensing agents to achieve varying DNA packaging densities and quantify DNA damage by free radical oxidation within the condensates. Although we see that tighter DNA packaging generally leads to better protection, the length of the polycation also plays a significant role. Molecular dynamics simulations suggest that longer polyarginine chains offer increased protection by occupying more space on the DNA surface and forming more stable interactions. Taken together, our results suggest a complex interplay among polycation properties, DNA packaging density, and DNA protection against free radical damage within condensed states.
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Affiliation(s)
- Ehigbai Oikeh
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Jesse Ziebarth
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
| | - Md Abu Monsur Dinar
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Daniel Kirchhoff
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Anastasiia Aronova
- Chemical and Materials Engineering Department, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Thomas D Dziubla
- Chemical and Materials Engineering Department, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yongmei Wang
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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2
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Love SD, Posey S, Burch AD, Fane BA. Disenfranchised DNA: biochemical analysis of mutant øX174 DNA-binding proteins may further elucidate the evolutionary significance of the unessential packaging protein A. J Virol 2024; 98:e0182723. [PMID: 38305183 PMCID: PMC10949513 DOI: 10.1128/jvi.01827-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
Most icosahedral DNA viruses package and condense their genomes into pre-formed, volumetrically constrained capsids. However, concurrent genome biosynthesis and packaging are specific to single-stranded (ss) DNA micro- and parvoviruses. Before packaging, ~120 copies of the øX174 DNA-binding protein J interact with double-stranded DNA. 60 J proteins enter the procapsid with the ssDNA genome, guiding it between 60 icosahedrally ordered DNA-binding pockets formed by the capsid proteins. Although J proteins are small, 28-37 residues in length, they have two domains. The basic, positively charged N-terminus guides the genome between binding pockets, whereas the C-terminus acts as an anchor to the capsid's inner surface. Three C-terminal aromatic residues, W30, Y31, and F37, interact most extensively with the coat protein. Their corresponding codons were mutated, and the resulting strains were biochemically and genetically characterized. Depending on the mutation, the substitutions produced unstable packaging complexes, unstable virions, infectious progeny, or particles packaged with smaller genomes, the latter being a novel phenomenon. The smaller genomes contained internal deletions. The juncture sequences suggest that the unessential A* (A star) protein mediates deletion formation.IMPORTANCEUnessential but strongly conserved gene products are understudied, especially when mutations do not confer discernable phenotypes or the protein's contribution to fitness is too small to reliably determine in laboratory-based assays. Consequently, their functions and evolutionary impact remain obscure. The data presented herein suggest that microvirus A* proteins, discovered over 40 years ago, may hasten the termination of non-productive packaging events. Thus, performing a salvage function by liberating the reusable components of the failed packaging complexes, such as DNA templates and replication enzymes.
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Affiliation(s)
- Samuel D. Love
- The BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Sierra Posey
- Berkshire School, Advanced Math/Science Research Program, Sheffield, Massachusetts, USA
| | - April D. Burch
- Berkshire School, Advanced Math/Science Research Program, Sheffield, Massachusetts, USA
| | - Bentley A. Fane
- The BIO5 Institute, University of Arizona, Tucson, Arizona, USA
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3
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Agarwal S, Osmanovic D, Dizani M, Klocke MA, Franco E. Dynamic control of DNA condensation. Nat Commun 2024; 15:1915. [PMID: 38429336 PMCID: PMC10907372 DOI: 10.1038/s41467-024-46266-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 02/21/2024] [Indexed: 03/03/2024] Open
Abstract
Artificial biomolecular condensates are emerging as a versatile approach to organize molecular targets and reactions without the need for lipid membranes. Here we ask whether the temporal response of artificial condensates can be controlled via designed chemical reactions. We address this general question by considering a model problem in which a phase separating component participates in reactions that dynamically activate or deactivate its ability to self-attract. Through a theoretical model we illustrate the transient and equilibrium effects of reactions, linking condensate response and reaction parameters. We experimentally realize our model problem using star-shaped DNA motifs known as nanostars to generate condensates, and we take advantage of strand invasion and displacement reactions to kinetically control the capacity of nanostars to interact. We demonstrate reversible dissolution and growth of DNA condensates in the presence of specific DNA inputs, and we characterize the role of toehold domains, nanostar size, and nanostar valency. Our results will support the development of artificial biomolecular condensates that can adapt to environmental changes with prescribed temporal dynamics.
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Affiliation(s)
- Siddharth Agarwal
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Bioengineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Dino Osmanovic
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Mahdi Dizani
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Melissa A Klocke
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Elisa Franco
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Bioengineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
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4
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Mukherjee A, Kizziah JL, Hawkins NC, Nasef MO, Parker LK, Dokland T. Structure of the Portal Complex from Staphylococcus aureus Pathogenicity Island 1 Transducing Particles In Situ and In Isolation. J Mol Biol 2024; 436:168415. [PMID: 38135177 PMCID: PMC10923094 DOI: 10.1016/j.jmb.2023.168415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal itself, produced by overexpression, and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.
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Affiliation(s)
- Amarshi Mukherjee
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - James L Kizziah
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - N'Toia C Hawkins
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Mohamed O Nasef
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Laura K Parker
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Terje Dokland
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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5
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Dasgupta S, Thomas JA, Ray K. Mechanism of Viral DNA Packaging in Phage T4 Using Single-Molecule Fluorescence Approaches. Viruses 2024; 16:192. [PMID: 38399968 PMCID: PMC10893049 DOI: 10.3390/v16020192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
In all tailed phages, the packaging of the double-stranded genome into the head by a terminase motor complex is an essential step in virion formation. Despite extensive research, there are still major gaps in the understanding of this highly dynamic process and the mechanisms responsible for DNA translocation. Over the last fifteen years, single-molecule fluorescence technologies have been applied to study viral nucleic acid packaging using the robust and flexible T4 in vitro packaging system in conjunction with genetic, biochemical, and structural analyses. In this review, we discuss the novel findings from these studies, including that the T4 genome was determined to be packaged as an elongated loop via the colocalization of dye-labeled DNA termini above the portal structure. Packaging efficiency of the TerL motor was shown to be inherently linked to substrate structure, with packaging stalling at DNA branches. The latter led to the design of multiple experiments whose results all support a proposed torsional compression translocation model to explain substrate packaging. Evidence of substrate compression was derived from FRET and/or smFRET measurements of stalled versus resolvase released dye-labeled Y-DNAs and other dye-labeled substrates relative to motor components. Additionally, active in vivo T4 TerS fluorescent fusion proteins facilitated the application of advanced super-resolution optical microscopy toward the visualization of the initiation of packaging. The formation of twin TerS ring complexes, each expected to be ~15 nm in diameter, supports a double protein ring-DNA synapsis model for the control of packaging initiation, a model that may help explain the variety of ring structures reported among pac site phages. The examination of the dynamics of the T4 packaging motor at the single-molecule level in these studies demonstrates the value of state-of-the-art fluorescent tools for future studies of complex viral replication mechanisms.
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Affiliation(s)
- Souradip Dasgupta
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Julie A. Thomas
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA;
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
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6
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Prokhorov NS, Davis C, Maruthi K, Yang Q, Sherman M, Woodson M, White M, Miller LM, Jarrold M, Catalano C, Morais M. Biophysical and structural characterization of a multifunctional viral genome packaging motor. Nucleic Acids Res 2024; 52:831-843. [PMID: 38084901 PMCID: PMC10810279 DOI: 10.1093/nar/gkad1135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 01/26/2024] Open
Abstract
The large dsDNA viruses replicate their DNA as concatemers consisting of multiple covalently linked genomes. Genome packaging is catalyzed by a terminase enzyme that excises individual genomes from concatemers and packages them into preassembled procapsids. These disparate tasks are catalyzed by terminase alternating between two distinct states-a stable nuclease that excises individual genomes and a dynamic motor that translocates DNA into the procapsid. It was proposed that bacteriophage λ terminase assembles as an anti-parallel dimer-of-dimers nuclease complex at the packaging initiation site. In contrast, all characterized packaging motors are composed of five terminase subunits bound to the procapsid in a parallel orientation. Here, we describe biophysical and structural characterization of the λ holoenzyme complex assembled in solution. Analytical ultracentrifugation, small angle X-ray scattering, and native mass spectrometry indicate that 5 subunits assemble a cone-shaped terminase complex. Classification of cryoEM images reveals starfish-like rings with skewed pentameric symmetry and one special subunit. We propose a model wherein nuclease domains of two subunits alternate between a dimeric head-to-head arrangement for genome maturation and a fully parallel arrangement during genome packaging. Given that genome packaging is strongly conserved in both prokaryotic and eukaryotic viruses, the results have broad biological implications.
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Affiliation(s)
- Nikolai S Prokhorov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Christal R Davis
- Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kashyap Maruthi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Qin Yang
- Department of Pharmaceutical Chemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Campus, Aurora, CO 80045, USA
| | - Michael B Sherman
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Michael Woodson
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Mark A White
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Lohra M Miller
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Carlos E Catalano
- Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pharmaceutical Chemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Campus, Aurora, CO 80045, USA
| | - Marc C Morais
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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7
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Nishiyama A, Shimizu M, Narita T, Kodera N, Ozeki Y, Yokoyama A, Mayanagi K, Yamaguchi T, Hakamata M, Shaban A, Tateishi Y, Ito K, Matsumoto S. Dynamic action of an intrinsically disordered protein in DNA compaction that induces mycobacterial dormancy. Nucleic Acids Res 2024; 52:816-830. [PMID: 38048321 PMCID: PMC10810275 DOI: 10.1093/nar/gkad1149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023] Open
Abstract
Mycobacteria are the major human pathogens with the capacity to become dormant persisters. Mycobacterial DNA-binding protein 1 (MDP1), an abundant histone-like protein in dormant mycobacteria, induces dormancy phenotypes, e.g. chromosome compaction and growth suppression. For these functions, the polycationic intrinsically disordered region (IDR) is essential. However, the disordered property of IDR stands in the way of clarifying the molecular mechanism. Here we clarified the molecular and structural mechanism of DNA compaction by MDP1. Using high-speed atomic force microscopy, we observed that monomeric MDP1 bundles two adjacent DNA duplexes side-by-side via IDR. Combined with coarse-grained molecular dynamics simulation, we revealed the novel dynamic DNA cross-linking model of MDP1 in which a stretched IDR cross-links two DNA duplexes like double-sided tape. IDR is able to hijack HU function, resulting in the induction of strong mycobacterial growth arrest. This IDR-mediated reversible DNA cross-linking is a reasonable model for MDP1 suppression of the genomic function in the resuscitable non-replicating dormant mycobacteria.
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Affiliation(s)
- Akihito Nishiyama
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Masahiro Shimizu
- Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1192, Japan
- Division of Quantum Beam Material Science, Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Tomoyuki Narita
- Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1192, Japan
| | - Noriyuki Kodera
- Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1192, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Akira Yokoyama
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Kouta Mayanagi
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takehiro Yamaguchi
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
- Department of Pharmacology, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan
| | - Mariko Hakamata
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
- Department of Respiratory Medicine and Infectious Disease, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Amina Kaboso Shaban
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Yoshitaka Tateishi
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Kosuke Ito
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata 950-2181, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
- Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Kampus C Jl. Mulyorejo, Surabaya, East Java 60115, Indonesia
- Division of Research Aids, Hokkaido University Institute for Vaccine Research & Development, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan
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8
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Golfier S, Quail T, Brugués J. Single-Molecule Approaches to Study DNA Condensation. Methods Mol Biol 2024; 2740:1-19. [PMID: 38393466 DOI: 10.1007/978-1-0716-3557-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Proteins drive genome compartmentalization across different length scales. While the identities of these proteins have been well-studied, the physical mechanisms that drive genome organization have remained largely elusive. Studying these mechanisms is challenging owing to a lack of methodologies to parametrize physical models in cellular contexts. Furthermore, because of the complex, entangled, and dense nature of chromatin, conventional live imaging approaches often lack the spatial resolution to dissect these principles. In this chapter, we will describe how to image the interactions of λ-DNA with proteins under purified and cytoplasmic conditions. First, we will outline how to prepare biotinylated DNA, functionalize coverslips with biotin-conjugated poly-ethylene glycol (PEG), and assemble DNA microchannels compatible for the imaging of protein-DNA interactions using total internal fluorescence microscopy. Then we will describe experimental methods to image protein-DNA interactions in vitro and DNA loop extrusion using Xenopus laevis egg extracts.
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Affiliation(s)
- Stefan Golfier
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
- B CUBE, Center for Molecular Bioengineering, TU Dresden, Dresden, Germany
| | - Thomas Quail
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
- EMBL Heidelberg, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | - Jan Brugués
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.
- Center for Systems Biology Dresden, Dresden, Germany.
- Physics of Life, TU Dresden, Dresden, Germany.
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9
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Abstract
The specialized packaging of sperm DNA preserves genome stability in the fruit fly zygote.
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Affiliation(s)
- Mia T Levine
- Department of Biology, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
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10
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Dubruille R, Herbette M, Revel M, Horard B, Chang CH, Loppin B. Histone removal in sperm protects paternal chromosomes from premature division at fertilization. Science 2023; 382:725-731. [PMID: 37943933 DOI: 10.1126/science.adh0037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/22/2023] [Indexed: 11/12/2023]
Abstract
The global replacement of histones with protamines in sperm chromatin is widespread in animals, including insects, but its actual function remains enigmatic. We show that in the Drosophila paternal effect mutant paternal loss (pal), sperm chromatin retains germline histones H3 and H4 genome wide without impairing sperm viability. However, after fertilization, pal sperm chromosomes are targeted by the egg chromosomal passenger complex and engage into a catastrophic premature division in synchrony with female meiosis II. We show that pal encodes a rapidly evolving transition protein specifically required for the eviction of (H3-H4)2 tetramers from spermatid DNA after the removal of H2A-H2B dimers. Our study thus reveals an unsuspected role of histone eviction from insect sperm chromatin: safeguarding the integrity of the male pronucleus during female meiosis.
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Affiliation(s)
- Raphaëlle Dubruille
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Marion Herbette
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Maxime Revel
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Béatrice Horard
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Ching-Ho Chang
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Benjamin Loppin
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Université Claude Bernard Lyon 1, Lyon, France
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11
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Mohana G, Dorier J, Li X, Mouginot M, Smith RC, Malek H, Leleu M, Rodriguez D, Khadka J, Rosa P, Cousin P, Iseli C, Restrepo S, Guex N, McCabe BD, Jankowski A, Levine MS, Gambetta MC. Chromosome-level organization of the regulatory genome in the Drosophila nervous system. Cell 2023; 186:3826-3844.e26. [PMID: 37536338 PMCID: PMC10529364 DOI: 10.1016/j.cell.2023.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 03/31/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
Abstract
Previous studies have identified topologically associating domains (TADs) as basic units of genome organization. We present evidence of a previously unreported level of genome folding, where distant TAD pairs, megabases apart, interact to form meta-domains. Within meta-domains, gene promoters and structural intergenic elements present in distant TADs are specifically paired. The associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. These long-range associations occur in a large fraction of neurons but support transcription in only a subset of neurons. Meta-domains are formed by diverse transcription factors that are able to pair over long and flexible distances. We present evidence that two such factors, GAF and CTCF, play direct roles in this process. The relative simplicity of higher-order meta-domain interactions in Drosophila, compared with those previously described in mammals, allowed the demonstration that genomes can fold into highly specialized cell-type-specific scaffolds that enable megabase-scale regulatory associations.
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Affiliation(s)
- Giriram Mohana
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Julien Dorier
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Center, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Xiao Li
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Marion Mouginot
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Rebecca C Smith
- Brain Mind Institute, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Héléna Malek
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marion Leleu
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Center, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Daniel Rodriguez
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jenisha Khadka
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Patrycja Rosa
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland
| | - Pascal Cousin
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Center, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Simon Restrepo
- Arcoris bio AG, Lüssirainstrasse 52, 6300 Zug, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Center, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Brian D McCabe
- Brain Mind Institute, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Aleksander Jankowski
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland.
| | - Michael S Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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12
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Hawkins DEDP, Bayfield O, Fung HKH, Grba DN, Huet A, Conway J, Antson AA. Insights into a viral motor: the structure of the HK97 packaging termination assembly. Nucleic Acids Res 2023; 51:7025-7035. [PMID: 37293963 PMCID: PMC10359639 DOI: 10.1093/nar/gkad480] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023] Open
Abstract
Double-stranded DNA viruses utilise machinery, made of terminase proteins, to package viral DNA into the capsid. For cos bacteriophage, a defined signal, recognised by small terminase, flanks each genome unit. Here we present the first structural data for a cos virus DNA packaging motor, assembled from the bacteriophage HK97 terminase proteins, procapsids encompassing the portal protein, and DNA containing a cos site. The cryo-EM structure is consistent with the packaging termination state adopted after DNA cleavage, with DNA density within the large terminase assembly ending abruptly at the portal protein entrance. Retention of the large terminase complex after cleavage of the short DNA substrate suggests that motor dissociation from the capsid requires headful pressure, in common with pac viruses. Interestingly, the clip domain of the 12-subunit portal protein does not adhere to C12 symmetry, indicating asymmetry induced by binding of the large terminase/DNA. The motor assembly is also highly asymmetric, showing a ring of 5 large terminase monomers, tilted against the portal. Variable degrees of extension between N- and C-terminal domains of individual subunits suggest a mechanism of DNA translocation driven by inter-domain contraction and relaxation.
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Affiliation(s)
- Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Herman K H Fung
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117Heidelberg, Germany
| | - Daniel N Grba
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Alexis Huet
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - James F Conway
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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13
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Deng L, Zhao Z, Liu L, Zhong Z, Xie W, Zhou F, Xu W, Zhang Y, Deng Z, Sun Y. Dissection of 3D chromosome organization in Streptomyces coelicolor A3(2) leads to biosynthetic gene cluster overexpression. Proc Natl Acad Sci U S A 2023; 120:e2222045120. [PMID: 36877856 PMCID: PMC10242723 DOI: 10.1073/pnas.2222045120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/08/2023] [Indexed: 03/08/2023] Open
Abstract
The soil-dwelling filamentous bacteria, Streptomyces, is widely known for its ability to produce numerous bioactive natural products. Despite many efforts toward their overproduction and reconstitution, our limited understanding of the relationship between the host's chromosome three dimension (3D) structure and the yield of the natural products escaped notice. Here, we report the 3D chromosome organization and its dynamics of the model strain, Streptomyces coelicolor, during the different growth phases. The chromosome undergoes a dramatic global structural change from primary to secondary metabolism, while some biosynthetic gene clusters (BGCs) form special local structures when highly expressed. Strikingly, transcription levels of endogenous genes are found to be highly correlated to the local chromosomal interaction frequency as defined by the value of the frequently interacting regions (FIREs). Following the criterion, an exogenous single reporter gene and even complex BGC can achieve a higher expression after being integrated into the chosen loci, which may represent a unique strategy to activate or enhance the production of natural products based on the local chromosomal 3D organization.
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Affiliation(s)
- Liang Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Zhihu Zhao
- Department of Protein Engineering, Beijing Institute of Biotechnology, Beijing100071, China
| | - Lin Liu
- Epigenetic Division, Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan430075, China
| | - Zhiyu Zhong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Wenxinyu Xie
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Fan Zhou
- Epigenetic Division, Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan430075, China
| | - Wei Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Yubo Zhang
- Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518120, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
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14
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Lokareddy RK, Hou CFD, Li F, Yang R, Cingolani G. Viral Small Terminase: A Divergent Structural Framework for a Conserved Biological Function. Viruses 2022; 14:v14102215. [PMID: 36298770 PMCID: PMC9611059 DOI: 10.3390/v14102215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022] Open
Abstract
The genome packaging motor of bacteriophages and herpesviruses is built by two terminase subunits, known as large (TerL) and small (TerS), both essential for viral genome packaging. TerL structure, composition, and assembly to an empty capsid, as well as the mechanisms of ATP-dependent DNA packaging, have been studied in depth, shedding light on the chemo-mechanical coupling between ATP hydrolysis and DNA translocation. Instead, significantly less is known about the small terminase subunit, TerS, which is dispensable or even inhibitory in vitro, but essential in vivo. By taking advantage of the recent revolution in cryo-electron microscopy (cryo-EM) and building upon a wealth of crystallographic structures of phage TerSs, in this review, we take an inventory of known TerSs studied to date. Our analysis suggests that TerS evolved and diversified into a flexible molecular framework that can conserve biological function with minimal sequence and quaternary structure conservation to fit different packaging strategies and environmental conditions.
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15
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Fung HKH, Grimes S, Huet A, Duda RL, Chechik M, Gault J, Robinson C, Hendrix R, Jardine P, Conway J, Baumann C, Antson A. Structural basis of DNA packaging by a ring-type ATPase from an archetypal viral system. Nucleic Acids Res 2022; 50:8719-8732. [PMID: 35947691 PMCID: PMC9410871 DOI: 10.1093/nar/gkac647] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/06/2022] [Accepted: 07/24/2022] [Indexed: 12/24/2022] Open
Abstract
Many essential cellular processes rely on substrate rotation or translocation by a multi-subunit, ring-type NTPase. A large number of double-stranded DNA viruses, including tailed bacteriophages and herpes viruses, use a homomeric ring ATPase to processively translocate viral genomic DNA into procapsids during assembly. Our current understanding of viral DNA packaging comes from three archetypal bacteriophage systems: cos, pac and phi29. Detailed mechanistic understanding exists for pac and phi29, but not for cos. Here, we reconstituted in vitro a cos packaging system based on bacteriophage HK97 and provided a detailed biochemical and structural description. We used a photobleaching-based, single-molecule assay to determine the stoichiometry of the DNA-translocating ATPase large terminase. Crystal structures of the large terminase and DNA-recruiting small terminase, a first for a biochemically defined cos system, reveal mechanistic similarities between cos and pac systems. At the same time, mutational and biochemical analyses indicate a new regulatory mechanism for ATPase multimerization and coordination in the HK97 system. This work therefore establishes a framework for studying the evolutionary relationships between ATP-dependent DNA translocation machineries in double-stranded DNA viruses.
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Affiliation(s)
- Herman K H Fung
- Department of Biology, University of York, York, YO10 5DD, UK
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Shelley Grimes
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alexis Huet
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Robert L Duda
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Roger W Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - James F Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | | | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
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16
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Serwer P. A Perspective on Studies of Phage DNA Packaging Dynamics. Int J Mol Sci 2022; 23:ijms23147854. [PMID: 35887200 PMCID: PMC9324371 DOI: 10.3390/ijms23147854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 12/05/2022] Open
Abstract
The Special Issue “DNA Packaging Dynamics of Bacteriophages” is focused on an event that is among the physically simplest known events with biological character. Thus, phage DNA (and RNA) packaging is used as a relatively accessible model for physical analysis of all biological events. A similar perspective motivated early phage-directed work, which was a major contributor to early molecular biology. However, analysis of DNA packaging encounters the limitation that phages vary in difficulty of observing various aspects of their packaging. If a difficult-to-access aspect arises while using a well-studied phage, a counterstrategy is to (1) look for and use phages that provide a better access “window” and (2) integrate multi-phage-accessed information with the help of chemistry and physics. The assumption is that all phages are characterized by the same evolution-derived themes, although with variations. Universal principles will emerge from the themes. A spin-off of using this strategy is the isolation and characterization of the diverse phages needed for biomedicine. Below, I give examples in the areas of infectious disease, cancer, and neurodegenerative disease.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry and Structural Biology, The University of Texas Health Center at San Antonio, San Antonio, TX 78229, USA
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17
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de Bruijn R, Wielstra PCM, Calcines-Cruz C, van Waveren T, Hernandez-Garcia A, van der Schoot P. A kinetic model for the impact of packaging signal mimics on genome encapsulation. Biophys J 2022; 121:2583-2599. [PMID: 35642255 DOI: 10.1016/j.bpj.2022.05.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/09/2022] [Accepted: 05/24/2022] [Indexed: 11/18/2022] Open
Abstract
Inspired by recent experiments on the spontaneous assembly of virus-like particles from a solution containing a synthetic coat protein and double-stranded DNA, we put forward a kinetic model that has as main ingredients a stochastic nucleation and a deterministic growth process. The efficiency and rate of DNA packaging strongly increase after tiling the DNA with CRISPR-Cas proteins at predesignated locations, mimicking assembly signals in viruses. Our model shows that treating these proteins as nucleation-inducing diffusion barriers is sufficient to explain the experimentally observed increase in encapsulation efficiency, but only if the nucleation rate is sufficiently high. We find an optimum in the encapsulation kinetics for conditions where the number of packaging signal mimics is equal to the number of nucleation events that can occur during the time required to fully encapsulate the DNA template, presuming that the nucleation events can only take place adjacent to a packaging signal. Our theory is in satisfactory agreement with the available experimental data.
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Affiliation(s)
- René de Bruijn
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, the Netherlands; Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
| | | | - Carlos Calcines-Cruz
- Department of Chemistry of Biomacromolecules, Institute of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - Tom van Waveren
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Armando Hernandez-Garcia
- Department of Chemistry of Biomacromolecules, Institute of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - Paul van der Schoot
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, the Netherlands
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18
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Abstract
Although the process of genome encapsidation is highly conserved in tailed bacteriophages and eukaryotic double-stranded DNA viruses, there are two distinct packaging pathways that these viruses use to catalyze ATP-driven translocation of the viral genome into a preassembled procapsid shell. One pathway is used by ϕ29-like phages and adenoviruses, which replicate and subsequently package a monomeric, unit-length genome covalently attached to a virus/phage-encoded protein at each 5'-end of the dsDNA genome. In a second, more ubiquitous packaging pathway characterized by phage lambda and the herpesviruses, the viral DNA is replicated as multigenome concatemers linked in a head-to-tail fashion. Genome packaging in these viruses thus requires excision of individual genomes from the concatemer that are then translocated into a preassembled procapsid. Hence, the ATPases that power packaging in these viruses also possess nuclease activities that cut the genome from the concatemer at the beginning and end of packaging. This review focuses on proposed mechanisms of genome packaging in the dsDNA viruses using unit-length ϕ29 and concatemeric λ genome packaging motors as representative model systems.
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Affiliation(s)
- Carlos E Catalano
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, United States.
| | - Marc C Morais
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, TX, United States
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19
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Naniima P, Naimo E, Koch S, Curth U, Alkharsah KR, Ströh LJ, Binz A, Beneke JM, Vollmer B, Böning H, Borst EM, Desai P, Bohne J, Messerle M, Bauerfeind R, Legrand P, Sodeik B, Schulz TF, Krey T. Assembly of infectious Kaposi's sarcoma-associated herpesvirus progeny requires formation of a pORF19 pentamer. PLoS Biol 2021; 19:e3001423. [PMID: 34735435 PMCID: PMC8568140 DOI: 10.1371/journal.pbio.3001423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 09/22/2021] [Indexed: 12/25/2022] Open
Abstract
Herpesviruses cause severe diseases particularly in immunocompromised patients. Both genome packaging and release from the capsid require a unique portal channel occupying one of the 12 capsid vertices. Here, we report the 2.6 Å crystal structure of the pentameric pORF19 of the γ-herpesvirus Kaposi’s sarcoma-associated herpesvirus (KSHV) resembling the portal cap that seals this portal channel. We also present the structure of its β-herpesviral ortholog, revealing a striking structural similarity to its α- and γ-herpesviral counterparts despite apparent differences in capsid association. We demonstrate pORF19 pentamer formation in solution and provide insights into how pentamerization is triggered in infected cells. Mutagenesis in its lateral interfaces blocked pORF19 pentamerization and severely affected KSHV capsid assembly and production of infectious progeny. Our results pave the way to better understand the role of pORF19 in capsid assembly and identify a potential novel drug target for the treatment of herpesvirus-induced diseases. In herpesviruses, genome packaging and release from the capsid require a unique portal channel. Here, the authors have resolved the crystal structure of a pentameric KSHV pORF19 assembly and find that it resembles the herpesviral portal cap and provides insights how the viral genome is retained within the capsid.
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Affiliation(s)
- Peter Naniima
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner sites Hannover-Braunschweig and Hamburg-Lübeck-Borstel-Riems, Braunschweig, Germany
| | - Eleonora Naimo
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner sites Hannover-Braunschweig and Hamburg-Lübeck-Borstel-Riems, Braunschweig, Germany
| | - Sandra Koch
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner sites Hannover-Braunschweig and Hamburg-Lübeck-Borstel-Riems, Braunschweig, Germany
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Khaled R. Alkharsah
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University (IAU), Dammam, Saudi Arabia
| | - Luisa J. Ströh
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Anne Binz
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, Hannover, Germany
| | - Jan-Marc Beneke
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany
| | - Benjamin Vollmer
- Centre for Structural Systems Biology, Leibniz-Institut für Experimentelle Virologie (HPI), Hamburg, Germany
| | - Heike Böning
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Eva Maria Borst
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Prashant Desai
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jens Bohne
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Martin Messerle
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner sites Hannover-Braunschweig and Hamburg-Lübeck-Borstel-Riems, Braunschweig, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, Hannover, Germany
| | - Rudolf Bauerfeind
- Research Core Unit Laser Microscopy, Hannover Medical School, Hannover, Germany
| | - Pierre Legrand
- Synchrotron SOLEIL, L’Orme des Merisiers, Gif-sur-Yvette, France
| | - Beate Sodeik
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner sites Hannover-Braunschweig and Hamburg-Lübeck-Borstel-Riems, Braunschweig, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, Hannover, Germany
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner sites Hannover-Braunschweig and Hamburg-Lübeck-Borstel-Riems, Braunschweig, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, Hannover, Germany
| | - Thomas Krey
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner sites Hannover-Braunschweig and Hamburg-Lübeck-Borstel-Riems, Braunschweig, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, Hannover, Germany
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- * E-mail:
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20
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Abstract
Nanomotors in nanotechnology may be as important as cars in daily life. Biomotors are nanoscale machines ubiquitous in living systems to carry out ATP-driven activities such as walking, breathing, blinking, mitosis, replication, transcription, and trafficking. The sequential action in an asymmetrical hexamer by a revolving mechanism has been confirmed in dsDNA packaging motors of phi29, herpesviruses, bacterial dsDNA translocase FtsK, and Streptomyces TraB for conjugative dsDNA transfer. These elaborate, delicate, and exquisite ring structures have inspired scientists to design biomimetics in nanotechnology. Many multisubunit ATPase rings generate force via sequential action of multiple modules, such as the Walker A, Walker B, P-loop, arginine finger, sensors, and lid. The chemical to mechanical energy conversion usually takes place in sequential order. It is commonly believed that ATP binding triggers such conversion, but how the multimodule motor starts the sequential process has not been explicitly investigated. Identification of the starter is of great significance for biomimetic motor fabrication. Here, we report that the arginine finger is the starter of the motor. Only one amino acid residue change in the arginine finger led to the impediment and elimination of all following steps. Without the arginine finger, the motor failed to assemble, bind ATP, recruit DNA, or hydrolyze ATP and was eventually unable to package DNA. However, the loss of ATPase activity due to an inactive arginine finger can be rescued by an arginine finger from the adjacent subunit of Walker A mutant through trans-complementation. Taken together, we demonstrate that the formation of dimers triggered by the arginine finger initiates the motor action rather than the general belief of initiation by ATP binding.
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Affiliation(s)
- Chenxi Liang
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy and
College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- James
Comprehensive Cancer Center, The Ohio State
University, Columbus, Ohio 43210, United States
- Dorothy
M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, United States
- Biomedical
Science Graduate Program, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Peixuan Guo
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy and
College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- James
Comprehensive Cancer Center, The Ohio State
University, Columbus, Ohio 43210, United States
- Dorothy
M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, United States
- Biomedical
Science Graduate Program, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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21
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Mukherjee A, de Izarra A, Degrouard J, Olive E, Maiti PK, Jang YH, Lansac Y. Protamine-Controlled Reversible DNA Packaging: A Molecular Glue. ACS Nano 2021; 15:13094-13104. [PMID: 34328301 DOI: 10.1021/acsnano.1c02337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Packaging paternal genome into tiny sperm nuclei during spermatogenesis requires 106-fold compaction of DNA, corresponding to a 10-20 times higher compaction than in somatic cells. While such a high level of compaction involves protamine, a small arginine-rich basic protein, the precise mechanism at play is still unclear. Effective pair potential calculations and large-scale molecular dynamics simulations using a simple idealized model incorporating solely electrostatic and steric interactions clearly demonstrate a reversible control on DNA condensates formation by varying the protamine-to-DNA ratio. Microscopic states and condensate structures occurring in semidilute solutions of short DNA fragments are in good agreement with experimental phase diagram and cryoTEM observations. The reversible microscopic mechanisms induced by protamination modulation should provide valuable information to improve a mechanistic understanding of early and intermediate stages of spermatogenesis where an interplay between condensation and liquid-liquid phase separation triggered by protamine expression and post-translational regulation might occur. Moreover, recent vaccines to prevent virus infections and cancers using protamine as a packaging and depackaging agent might be fine-tuned for improved efficiency using a protamination control.
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Affiliation(s)
- Arnab Mukherjee
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
| | - Ambroise de Izarra
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
- Department of Energy Science and Engineering, DGIST, Daegu 42988, Korea
| | - Jeril Degrouard
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Saclay, 91405 Orsay, France
| | - Enrick Olive
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
| | - Yun Hee Jang
- Department of Energy Science and Engineering, DGIST, Daegu 42988, Korea
| | - Yves Lansac
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
- Department of Energy Science and Engineering, DGIST, Daegu 42988, Korea
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Saclay, 91405 Orsay, France
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22
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Abstract
Immediately following the discovery of the structure of DNA and the semi-conservative replication of the parental DNA sequence into two new DNA strands, it became apparent that DNA replication is organized in a temporal and spatial fashion during the S phase of the cell cycle, correlated with the large-scale organization of chromatin in the nucleus. After many decades of limited progress, technological advances in genomics, genome engineering, and imaging have finally positioned the field to tackle mechanisms underpinning the temporal and spatial regulation of DNA replication and the causal relationships between DNA replication and other features of large-scale chromosome structure and function. In this review, we discuss these major recent discoveries as well as expectations for the coming decade.
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Affiliation(s)
- Athanasios E Vouzas
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
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23
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Abstract
Genomic information is encoded on long strands of DNA, which are folded into chromatin and stored in a tiny nucleus. Nuclear chromatin is a negatively charged polymer composed of DNA, histones, and various nonhistone proteins. Because of its highly charged nature, chromatin structure varies greatly depending on the surrounding environment (e.g., cations, molecular crowding, etc.). New technologies to capture chromatin in living cells have been developed over the past 10 years. Our view on chromatin organization has drastically shifted from a regular and static one to a more variable and dynamic one. Chromatin forms numerous compact dynamic domains that act as functional units of the genome in higher eukaryotic cells and locally appear liquid-like. By changing DNA accessibility, these domains can govern various functions. Based on new evidences from versatile genomics and advanced imaging studies, we discuss the physical nature of chromatin in the crowded nuclear environment and how it is regulated.
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Affiliation(s)
- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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24
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Woodson M, Pajak J, Mahler BP, Zhao W, Zhang W, Arya G, White MA, Jardine PJ, Morais MC. A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA. Sci Adv 2021; 7:7/19/eabc1955. [PMID: 33962953 PMCID: PMC8104870 DOI: 10.1126/sciadv.abc1955] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Molecular segregation and biopolymer manipulation require the action of molecular motors to do work by applying directional forces to macromolecules. The additional strand conserved E (ASCE) ring motors are an ancient family of molecular motors responsible for diverse biological polymer manipulation tasks. Viruses use ASCE segregation motors to package their genomes into their protein capsids and provide accessible experimental systems due to their relative simplicity. We show by cryo-EM-focused image reconstruction that ASCE ATPases in viral double-stranded DNA (dsDNA) packaging motors adopt helical symmetry complementary to their dsDNA substrates. Together with previous data, our results suggest that these motors cycle between helical and planar configurations, providing a possible mechanism for directional translocation of DNA. Similar changes in quaternary structure have been observed for proteasome and helicase motors, suggesting an ancient and common mechanism of force generation that has been adapted for specific tasks over the course of evolution.
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Affiliation(s)
- Michael Woodson
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Joshua Pajak
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Bryon P Mahler
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Wei Zhao
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wei Zhang
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Characterization Facility, College of Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Mark A White
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Marc C Morais
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
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25
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Reyes-Aldrete E, Dill EA, Bussetta C, Szymanski MR, Diemer G, Maindola P, White MA, Bujalowski WM, Choi KH, Morais MC. Biochemical and Biophysical Characterization of the ds DNA Packaging Motor from the Lactococcus lactis Bacteriophage Asccphi28. Viruses 2020; 13:E15. [PMID: 33374840 PMCID: PMC7823558 DOI: 10.3390/v13010015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/16/2020] [Accepted: 12/16/2020] [Indexed: 02/07/2023] Open
Abstract
Double-stranded DNA viruses package their genomes into pre-assembled protein procapsids. This process is driven by macromolecular motors that transiently assemble at a unique vertex of the procapsid and utilize homomeric ring ATPases to couple genome encapsidation to ATP hydrolysis. Here, we describe the biochemical and biophysical characterization of the packaging ATPase from Lactococcus lactis phage asccφ28. Size-exclusion chromatography (SEC), analytical ultracentrifugation (AUC), small angle X-ray scattering (SAXS), and negative stain transmission electron microscopy (TEM) indicate that the ~45 kDa protein formed a 443 kDa cylindrical assembly with a maximum dimension of ~155 Å and radius of gyration of ~54 Å. Together with the dimensions of the crystallographic asymmetric unit from preliminary X-ray diffraction experiments, these results indicate that gp11 forms a decameric D5-symmetric complex consisting of two pentameric rings related by 2-fold symmetry. Additional kinetic analysis shows that recombinantly expressed gp11 has ATPase activity comparable to that of functional ATPase rings assembled on procapsids in other genome packaging systems. Hence, gp11 forms rings in solution that likely reflect the fully assembled ATPases in active virus-bound motor complexes. Whereas ATPase functionality in other double-stranded DNA (dsDNA) phage packaging systems requires assembly on viral capsids, the ability to form functional rings in solution imparts gp11 with significant advantages for high-resolution structural studies and rigorous biophysical/biochemical analysis.
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Affiliation(s)
- Emilio Reyes-Aldrete
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Erik A. Dill
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Cecile Bussetta
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Michal R. Szymanski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Geoffrey Diemer
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Priyank Maindola
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Mark A. White
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Wlodzimierz M. Bujalowski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Kyung H. Choi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Marc C. Morais
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
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26
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Abstract
Double-stranded DNA is under extreme confinement when packed in phage phi29 with osmotic pressures approaching 60 atm and densities near liquid crystalline. The shape of the capsid determined from experiment is elongated. We consider the effects of the capsid shape and volume on the DNA distribution. We propose simple models for the capsid of phage phi29 to capture volume, shape, and wall flexibility, leading to an accurate DNA density profile. The effect of the packaging motor twisting the DNA on the resulting density distribution has been explored. We find packing motor induced twisting leads to a greater numbers of defects formed. The emergence of defects such as bubbles or large roll angles along the DNA shows a sequence dependence, and the resulting flexibility leads to an inhomogeneous distribution of defects occurring more often at TpA steps and AT-rich regions. In conjunction with capsid elongation, this has effects on the global DNA packing structures.
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Affiliation(s)
- Cecilia Bores
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| | - Michael Woodson
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| | - Marc C Morais
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| | - B Montgomery Pettitt
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
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27
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Mahler BP, Bujalowski PJ, Mao H, Dill EA, Jardine PJ, Choi K, Morais MC. NMR structure of a vestigial nuclease provides insight into the evolution of functional transitions in viral ds DNA packaging motors. Nucleic Acids Res 2020; 48:11737-11749. [PMID: 33089330 PMCID: PMC7672431 DOI: 10.1093/nar/gkaa874] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/22/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023] Open
Abstract
Double-stranded DNA viruses use ATP-powered molecular motors to package their genomic DNA. To ensure efficient genome encapsidation, these motors regulate functional transitions between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the bacteriophage phi29 ATPase (CTD) that suggest a structural basis for these functional transitions. Sedimentation experiments show that the inter-domain linker in the full-length protein promotes oligomerization and thus may play a role in assembly of the functional motor. The NMR solution structure of the CTD indicates it is a vestigial nuclease domain that likely evolved from conserved nuclease domains in phage terminases. Despite the loss of nuclease activity, fluorescence binding assays confirm the CTD retains its DNA binding capabilities and fitting the CTD into cryoEM density of the phi29 motor shows that the CTD directly binds DNA. However, the interacting residues differ from those identified by NMR titration in solution, suggesting that packaging motors undergo conformational changes to transition between initiation, translocation, and termination. Taken together, these results provide insight into the evolution of functional transitions in viral dsDNA packaging motors.
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Affiliation(s)
- Bryon P Mahler
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Paul J Bujalowski
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Huzhang Mao
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Erik A Dill
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kyung H Choi
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Marc C Morais
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
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28
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Wu W, Cheng N, Black LW, Dietz H, Steven AC. Biphasic Packing of DNA and Internal Proteins in Bacteriophage T4 Heads Revealed by Bubblegram Imaging. Viruses 2020; 12:v12111282. [PMID: 33182609 PMCID: PMC7697877 DOI: 10.3390/v12111282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 11/17/2022] Open
Abstract
The virions of tailed bacteriophages and the evolutionarily related herpesviruses contain, in addition to highly condensed DNA, substantial quantities of internal proteins. These proteins (“ejection proteins”) have roles in scaffolding, maturational proteolysis, and cell-to-cell delivery. Whereas capsids are amenable to analysis at high resolution by cryo-electron microscopy, internal proteins have proved difficult to localize. In this study, we investigated the distribution of internal proteins in T4 by bubblegram imaging. Prior work has shown that at suitably high electron doses, radiation damage generates bubbles of hydrogen gas in nucleoprotein specimens. Using DNA origami as a test specimen, we show that DNA does not bubble under these conditions; it follows that bubbles represent markers for proteins. The interior of the prolate T4 head, ~1000 Å long by ~750 Å wide, has a bubble-free zone that is ~100–110 Å thick, underlying the capsid shell from which proteins are excluded by highly ordered DNA. Inside this zone, which is plausibly occupied by ~4 layers of coaxial spool, bubbles are generated at random locations in a disordered ensemble of internal proteins and the remainder of the genome.
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Affiliation(s)
- Weimin Wu
- Laboratory of Structural Biology Research, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892-8025, USA;
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892-8025, USA;
| | - Lindsay W. Black
- Department of Biochemistry and Molecular Biology, University of Maryland Medical School, Baltimore, MD 21201-1503, USA;
| | - Hendrik Dietz
- Physics Department, Technische Universität München, 85748 Garching-bei-München, Germany;
| | - Alasdair C. Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892-8025, USA;
- Correspondence: ; Tel.: +1-(301)-496-0132; Fax: +1-(301)-443-7651
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29
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Dedeo CL, Teschke CM, Alexandrescu AT. Keeping It Together: Structures, Functions, and Applications of Viral Decoration Proteins. Viruses 2020; 12:v12101163. [PMID: 33066635 PMCID: PMC7602432 DOI: 10.3390/v12101163] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/09/2020] [Accepted: 10/11/2020] [Indexed: 12/14/2022] Open
Abstract
Decoration proteins are viral accessory gene products that adorn the surfaces of some phages and viral capsids, particularly tailed dsDNA phages. These proteins often play a "cementing" role, reinforcing capsids against accumulating internal pressure due to genome packaging, or environmental insults such as extremes of temperature or pH. Many decoration proteins serve alternative functions, including target cell recognition, participation in viral assembly, capsid size determination, or modulation of host gene expression. Examples that currently have structures characterized to high-resolution fall into five main folding motifs: β-tulip, β-tadpole, OB-fold, Ig-like, and a rare knotted α-helical fold. Most of these folding motifs have structure homologs in virus and target cell proteins, suggesting horizontal gene transfer was important in their evolution. Oligomerization states of decoration proteins range from monomers to trimers, with the latter most typical. Decoration proteins bind to a variety of loci on capsids that include icosahedral 2-, 3-, and 5-fold symmetry axes, as well as pseudo-symmetry sites. These binding sites often correspond to "weak points" on the capsid lattice. Because of their unique abilities to bind virus surfaces noncovalently, decoration proteins are increasingly exploited for technology, with uses including phage display, viral functionalization, vaccination, and improved nanoparticle design for imaging and drug delivery. These applications will undoubtedly benefit from further advances in our understanding of these versatile augmenters of viral functions.
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30
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Zhang Z, Zhan Z, Wang B, Chen Y, Chen X, Wan C, Fu Y, Huang L. Archaeal Chromatin Proteins Cren7 and Sul7d Compact DNA by Bending and Bridging. mBio 2020; 11:e00804-20. [PMID: 32518188 PMCID: PMC7373190 DOI: 10.1128/mbio.00804-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/06/2020] [Indexed: 11/20/2022] Open
Abstract
Archaeal chromatin proteins Cren7 and Sul7d from Sulfolobus are DNA benders. To better understand their architectural roles in chromosomal DNA organization, we analyzed DNA compaction by Cren7 and Sis7d, a Sul7d family member, from Sulfolobus islandicus at the single-molecule (SM) level by total single-molecule internal reflection fluorescence microscopy (SM-TIRFM) and atomic force microscopy (AFM). We show that both Cren7 and Sis7d were able to compact singly tethered λ DNA into a highly condensed structure in a three-step process and that Cren7 was over an order of magnitude more efficient than Sis7d in DNA compaction. The two proteins were similar in DNA bending kinetics but different in DNA condensation patterns. At saturating concentrations, Sis7d formed randomly distributed clusters whereas Cren7 generated a single and highly condensed core on plasmid DNA. This observation is consistent with the greater ability of Cren7 than of Sis7d to bridge DNA. Our results offer significant insights into the mechanism and kinetics of chromosomal DNA organization in Crenarchaea.IMPORTANCE A long-standing question is how chromosomal DNA is packaged in Crenarchaeota, a major group of archaea, which synthesize large amounts of unique small DNA-binding proteins but in general contain no archaeal histones. In the present work, we tested our hypothesis that the two well-studied crenarchaeal chromatin proteins Cren7 and Sul7d compact DNA by both DNA bending and bridging. We show that the two proteins are capable of compacting DNA, albeit with different efficiencies and in different manners, at the single molecule level. We demonstrate for the first time that the two proteins, which have long been regarded as DNA binders and benders, are able to mediate DNA bridging, and this previously unknown property of the proteins allows DNA to be packaged into highly condensed structures. Therefore, our results provide significant insights into the mechanism and kinetics of chromosomal DNA organization in Crenarchaeota.
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Affiliation(s)
- Zhenfeng Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhengyan Zhan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bing Wang
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yuanyuan Chen
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiuqiang Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Cuihong Wan
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yu Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
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31
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Mayerova N, Cipak L, Gregan J. Cohesin Biology: From Passive Rings to Molecular Motors. Trends Genet 2020; 36:387-389. [PMID: 32396831 DOI: 10.1016/j.tig.2020.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/29/2020] [Accepted: 03/08/2020] [Indexed: 02/04/2023]
Abstract
The loop extrusion hypothesis postulated that extrusion of DNA loops through cohesin rings organizes genomes. Recent findings suggest that cohesin itself is a molecular motor that extrudes DNA. This has important implications not only for the organization of interphase chromatin but also for other processes where cohesin plays vital roles.
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Affiliation(s)
- Nina Mayerova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Lubos Cipak
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia
| | - Juraj Gregan
- Advanced Microscopy Facility, VBCF, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria; Department of Chromosome Biology, MPL, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
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32
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Black LW, Yan B, Ray K. The T4 TerL Prohead Packaging Motor Does Not Drive DNA Translocation by a Proposed Dehydration Mechanism. Viruses 2020; 12:v12050522. [PMID: 32397493 PMCID: PMC7291337 DOI: 10.3390/v12050522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
A "DNA crunching" linear motor mechanism that employs a grip-and-release transient spring like compression of B- to A-form DNA has been found in our previous studies. Our FRET measurements in vitro show a decrease in distance from TerL to portal during packaging; furthermore, there is a decrease in distance between closely positioned dye pairs in the Y-stem of translocating Y-DNA that conforms to B- and A- structure. In normal translocation into the prohead the TerL motor expels all B-form tightly binding YOYO-1 dye that cannot bind A-form. The TerL motor cannot package A-form dsRNA. Our work reported here shows that addition of helper B form DNA:DNA (D:D) 20mers allows increased packaging of heteroduplex A-form DNA:RNA 20mers (D:R), evidence for a B- to A-form spring motor pushing duplex nucleic acid. A-form DNA:RNA 25mers, 30mers, and 35mers alone are efficiently packaged into proheads by the TerL motor showing that a proposed hypothetical dehydration motor mechanism operating on duplex substrates does not provide the packaging motor force. Taken together with our previous studies showing TerL motor protein motion toward the portal during DNA packaging, our present studies of short D:D and D:R duplex nucleic acid substrates strongly supports our previous evidence that the protein motor pushes rather than pulls or dehydrates duplex substrates to provide the translocation into prohead packaging force.
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Affiliation(s)
- Lindsay W. Black
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (B.Y.); (K.R.)
- Correspondence:
| | - Bingxue Yan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (B.Y.); (K.R.)
| | - Krishanu Ray
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (B.Y.); (K.R.)
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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33
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Cruz B, Zhu Z, Calderer C, Arsuaga J, Vazquez M. Quantitative Study of the Chiral Organization of the Phage Genome Induced by the Packaging Motor. Biophys J 2020; 118:2103-2116. [PMID: 32353255 PMCID: PMC7203069 DOI: 10.1016/j.bpj.2020.03.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/04/2019] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
Molecular motors that translocate DNA are ubiquitous in nature. During morphogenesis of double-stranded DNA bacteriophages, a molecular motor drives the viral genome inside a protein capsid. Several models have been proposed for the three-dimensional geometry of the packaged genome, but very little is known of the signature of the molecular packaging motor. For instance, biophysical experiments show that in some systems, DNA rotates during the packaging reaction, but most current biophysical models fail to incorporate this property. Furthermore, studies including rotation mechanisms have reached contradictory conclusions. In this study, we compare the geometrical signatures imposed by different possible mechanisms for the packaging motors: rotation, revolution, and rotation with revolution. We used a previously proposed kinetic Monte Carlo model of the motor, combined with Brownian dynamics simulations of DNA to simulate deterministic and stochastic motor models. We find that rotation is necessary for the accumulation of DNA writhe and for the chiral organization of the genome. We observe that although in the initial steps of the packaging reaction, the torsional strain of the genome is released by rotation of the molecule, in the later stages, it is released by the accumulation of writhe. We suggest that the molecular motor plays a key role in determining the final structure of the encapsidated genome in bacteriophages.
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Affiliation(s)
- Brian Cruz
- Department of Mathematics, University of California, Berkeley, California
| | - Zihao Zhu
- Department of Microbiology and Molecular Genetics, University of California at Davis, Davis, California
| | - Carme Calderer
- School of Mathematics, University of Minnesota, Minneapolis, Minnesota
| | - Javier Arsuaga
- Department of Mathematics, University of California at Davis, Davis, California; Department of Molecular and Cellular Biology, University of California at Davis, Davis, California.
| | - Mariel Vazquez
- Department of Microbiology and Molecular Genetics, University of California at Davis, Davis, California; Department of Mathematics, University of California at Davis, Davis, California.
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Hognon C, Garaude S, Timmins J, Chipot C, Dehez F, Monari A. Molecular Bases of DNA Packaging in Bacteria Revealed by All-Atom Molecular Dynamics Simulations: The Case of Histone-Like Proteins in Borrelia burgdorferi. J Phys Chem Lett 2019; 10:7200-7207. [PMID: 31693374 DOI: 10.1021/acs.jpclett.9b02978] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA compaction is essential to ensure the packaging of the genetic material in living cells and also plays a key role in the epigenetic regulation of gene expression. In both humans and bacteria, DNA packaging is achieved by specific well-conserved proteins. Here, by means of all-atom molecular dynamics simulations, including the determination of relevant free-energy profiles, we rationalize the molecular bases for this remarkable process in bacteria, illustrating the crucial role played by positively charged amino acids of a small histone-like protein. We also present compelling evidence that this histone-like protein alone can induce strong bending of a DNA duplex around its core domain, a process that requires overcoming a major free-energy barrier.
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Affiliation(s)
- Cécilia Hognon
- Université de Lorraine and CNRS, LPCT UMR 7019 , F-54000 Nancy , France
| | - Simon Garaude
- Université de Lorraine and CNRS, LPCT UMR 7019 , F-54000 Nancy , France
| | - Joanna Timmins
- Université Grenoble Alpes , CNRS, CEA, IBS , F-38000 Grenoble , France
| | - Christophe Chipot
- Université de Lorraine and CNRS, LPCT UMR 7019 , F-54000 Nancy , France
- Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign , 54506 Vandoeuvre-lès-Nancy Cedex, France
| | - François Dehez
- Université de Lorraine and CNRS, LPCT UMR 7019 , F-54000 Nancy , France
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign , 54506 Vandoeuvre-lès-Nancy Cedex, France
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019 , F-54000 Nancy , France
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Dixit AB, Ray K, Black LW. A viral small terminase subunit (TerS) twin ring pac synapsis DNA packaging model is supported by fluorescent fusion proteins. Virology 2019; 536:39-48. [PMID: 31400548 PMCID: PMC6760839 DOI: 10.1016/j.virol.2019.07.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/23/2022]
Abstract
A bacteriophage T4 DNA "synapsis model" proposes that the bacteriophage T4 terminase small subunit (TerS) apposes two pac site containing dsDNA homologs to gauge concatemer maturation adequate for packaging initiation. N-terminus, C-terminus, or both ends modified fusion Ter S proteins retain function. Replacements of the TerS gene in the T4 genome with fusion genes encoding larger (18-45 kDa) TerS-eGFP and TerS-mCherry fluorescent fusion proteins function without significant change in phenotype. Co-infection and co-expression by T4 phages encoding TerS-eGFP and TerS-mCherry shows in vivo FRET in infected bacteria comparable to that of the purified, denatured and then renatured, mixed fusion proteins in vitro. FRET of purified, denatured-renatured, mixed temperature sensitive and native TerS fusion proteins at low and high temperature in vitro shows that TerS ring-like oligomer formation is essential for function in vivo. Super-resolution STORM and PALM microscopy of intercalating dye YOYO-1 DNA and photoactivatable TerS-PAmCherry-C1 fusions support accumulation of TerS dimeric or multiple ring-like oligomer structures containing DNA and gp16-mCherry in vivo as well as in vitro to regulate pac site cutting.
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Affiliation(s)
- Aparna Banerjee Dixit
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Krishanu Ray
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lindsay W Black
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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36
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Gong D, Dai X, Jih J, Liu YT, Bi GQ, Sun R, Zhou ZH. DNA-Packing Portal and Capsid-Associated Tegument Complexes in the Tumor Herpesvirus KSHV. Cell 2019; 178:1329-1343.e12. [PMID: 31447177 PMCID: PMC6753055 DOI: 10.1016/j.cell.2019.07.035] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/16/2019] [Accepted: 07/17/2019] [Indexed: 01/07/2023]
Abstract
Assembly of Kaposi's sarcoma-associated herpesvirus (KSHV) begins at a bacteriophage-like portal complex that nucleates formation of an icosahedral capsid with capsid-associated tegument complexes (CATCs) and facilitates translocation of an ∼150-kb dsDNA genome, followed by acquisition of a pleomorphic tegument and envelope. Because of deviation from icosahedral symmetry, KSHV portal and tegument structures have largely been obscured in previous studies. Using symmetry-relaxed cryo-EM, we determined the in situ structure of the KSHV portal and its interactions with surrounding capsid proteins, CATCs, and the terminal end of KSHV's dsDNA genome. Our atomic models of the portal and capsid/CATC, together with visualization of CATCs' variable occupancy and alternate orientation of CATC-interacting vertex triplexes, suggest a mechanism whereby the portal orchestrates procapsid formation and asymmetric long-range determination of CATC attachment during DNA packaging prior to pleomorphic tegumentation/envelopment. Structure-based mutageneses confirm that a triplex deep binding groove for CATCs is a hotspot that holds promise for antiviral development.
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Affiliation(s)
- Danyang Gong
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xinghong Dai
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jonathan Jih
- California NanoSystems Institute (CNSI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yun-Tao Liu
- California NanoSystems Institute (CNSI), University of California, Los Angeles, Los Angeles, CA 90095, USA; Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China (USTC), Hefei, Anhui 230026, China
| | - Guo-Qiang Bi
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China (USTC), Hefei, Anhui 230026, China
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute (CNSI), University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute (CNSI), University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Cuervo A, Fàbrega-Ferrer M, Machón C, Conesa JJ, Fernández FJ, Pérez-Luque R, Pérez-Ruiz M, Pous J, Vega MC, Carrascosa JL, Coll M. Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism. Nat Commun 2019; 10:3746. [PMID: 31431626 PMCID: PMC6702177 DOI: 10.1038/s41467-019-11705-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/18/2019] [Indexed: 12/31/2022] Open
Abstract
Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been packaged, the tail components assemble on the portal to render the mature infective virion. The tail tightly seals the ejection conduit until infection, when its interaction with the host membrane triggers the opening of the channel and the viral genome is delivered to the host cell. Using high-resolution cryo-electron microscopy and X-ray crystallography, here we describe various structures of the T7 bacteriophage portal and fiber-less tail complex, which suggest a possible mechanism for DNA retention and ejection: a portal closed conformation temporarily retains the genome before the tail is assembled, whereas an open portal is found in the tail. Moreover, a fold including a seven-bladed β-propeller domain is described for the nozzle tail protein.
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Affiliation(s)
- Ana Cuervo
- Centro Nacional de Biotecnología, (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Montserrat Fàbrega-Ferrer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Cristina Machón
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10, 08028, Barcelona, Spain
| | - José Javier Conesa
- Centro Nacional de Biotecnología, (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Francisco J Fernández
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
- Abvance Biotech srl, Ave. Reina Victoria 32, 28003, Madrid, Spain
| | - Rosa Pérez-Luque
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Mar Pérez-Ruiz
- Centro Nacional de Biotecnología, (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Joan Pous
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - M Cristina Vega
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - José L Carrascosa
- Centro Nacional de Biotecnología, (CNB-CSIC), Darwin 3, 28049, Madrid, Spain.
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain.
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10, 08028, Barcelona, Spain.
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38
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Yang L, Yang Q, Wang M, Jia R, Chen S, Zhu D, Liu M, Wu Y, Zhao X, Zhang S, Liu Y, Yu Y, Zhang L, Chen X, Cheng A. Terminase Large Subunit Provides a New Drug Target for Herpesvirus Treatment. Viruses 2019; 11:v11030219. [PMID: 30841485 PMCID: PMC6466031 DOI: 10.3390/v11030219] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/23/2019] [Accepted: 02/27/2019] [Indexed: 12/26/2022] Open
Abstract
Herpesvirus infection is an orderly, regulated process. Among these viruses, the encapsidation of viral DNA is a noteworthy link; the entire process requires a powered motor that binds to viral DNA and carries it into the preformed capsid. Studies have shown that this power motor is a complex composed of a large subunit, a small subunit, and a third subunit, which are collectively known as terminase. The terminase large subunit is highly conserved in herpesvirus. It mainly includes two domains: the C-terminal nuclease domain, which cuts the viral concatemeric DNA into a monomeric genome, and the N-terminal ATPase domain, which hydrolyzes ATP to provide energy for the genome cutting and transfer activities. Because this process is not present in eukaryotic cells, it provides a reliable theoretical basis for the development of safe and effective anti-herpesvirus drugs. This article reviews the genetic characteristics, protein structure, and function of the herpesvirus terminase large subunit, as well as the antiviral drugs that target the terminase large subunit. We hope to provide a theoretical basis for the prevention and treatment of herpesvirus.
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Affiliation(s)
- Linlin Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Dekang Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Xiaoyue Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, Sichuan, China.
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39
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Schwartz U, Németh A, Diermeier S, Exler JH, Hansch S, Maldonado R, Heizinger L, Merkl R, Längst G. Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin. Nucleic Acids Res 2019; 47:1239-1254. [PMID: 30496478 PMCID: PMC6379673 DOI: 10.1093/nar/gky1203] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/17/2018] [Accepted: 11/22/2018] [Indexed: 12/22/2022] Open
Abstract
Packaging of DNA into chromatin regulates DNA accessibility and consequently all DNA-dependent processes. The nucleosome is the basic packaging unit of DNA forming arrays that are suggested, by biochemical studies, to fold hierarchically into ordered higher-order structures of chromatin. This organization has been recently questioned using microscopy techniques, proposing an irregular structure. To address the principles of chromatin organization, we applied an in situ differential MNase-seq strategy and analyzed in silico the results of complete and partial digestions of human chromatin. We investigated whether different levels of chromatin packaging exist in the cell. We assessed the accessibility of chromatin within distinct domains of kb to Mb genomic regions, performed statistical analyses and computer modelling. We found no difference in MNase accessibility, suggesting no difference in fiber folding between domains of euchromatin and heterochromatin or between other sequence and epigenomic features of chromatin. Thus, our data suggests the absence of differentially organized domains of higher-order structures of chromatin. Moreover, we identified only local structural changes, with individual hyper-accessible nucleosomes surrounding regulatory elements, such as enhancers and transcription start sites. The regulatory sites per se are occupied with structurally altered nucleosomes, exhibiting increased MNase sensitivity. Our findings provide biochemical evidence that supports an irregular model of large-scale chromatin organization.
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Affiliation(s)
- Uwe Schwartz
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
| | - Attila Németh
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
| | - Sarah Diermeier
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
| | - Josef H Exler
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
| | - Stefan Hansch
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
| | - Rodrigo Maldonado
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
| | - Leonhard Heizinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Gernot Längst
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
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Abstract
Epidemiological studies report an increase of pathologies of male reproductive tracts and suggest a link between this trend and the increased exposure of men to endocrine disruptors (EDs). The mechanisms by which EDs impact male fertility are far to be elucidated although DNA, chromatin and epigenome of spermatozoa appear to be relevant targets for these molecules. Indeed, many studies report associations between increased levels of sperm DNA fragmentation (sDF) or aberrant chromatin condensation or epigenetic modifications and poor semen quality and/or infertile phenotype. In this scenario, therapies able to reduce sperm damage to DNA, chromatin and epigenome are sought. Currently, antioxidants and FSH administration is proposed for treating high levels of sDF, but whether or not such therapies are really effective is still debated. Further studies are necessary to understand the link between endocrine disruptor exposure and damage to sperm function and/or structure and thus to define effective therapeutic strategies.
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Affiliation(s)
- Monica Muratori
- Department of Experimental, Clinical and Biomedical Sciences, Unit of Sexual Medicine and Andrology, Center of Excellence DeNothe, University of Florence, Viale Pieraccini, 6, I-50139, Firenze, Italy.
| | - Christian De Geyter
- Reproductive Medicine and Gynecological Endocrinology (RME), University Hospital, University of Basel, Vogesenstrasse 134, CH-4031, Basel, Switzerland.
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41
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Kundu TK, Sikder S. Evolution of genome organization and epigenetic machineries. J Biosci 2018; 43:239-242. [PMID: 29872012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur,Bengaluru 560 064, India,
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42
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Abstract
It's the stuff of life, and we're fascinated by DNA and how it's packaged into chromatin and compacted into chromosomes. Advances in looking at chromatin organization in cells are letting us see this polymer, its packing, and its function with fresh eyes.
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43
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Serwer P, Wright ET. ATP-Driven Contraction of Phage T3 Capsids with DNA Incompletely Packaged In Vivo. Viruses 2017; 9:v9050119. [PMID: 28534826 PMCID: PMC5454431 DOI: 10.3390/v9050119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/01/2017] [Accepted: 05/10/2017] [Indexed: 02/07/2023] Open
Abstract
Adenosine triphosphate (ATP) cleavage powers packaging of a double-stranded DNA (dsDNA) molecule in a pre-assembled capsid of phages that include T3. Several observations constitute a challenge to the conventional view that the shell of the capsid is energetically inert during packaging. Here, we test this challenge by analyzing the in vitro effects of ATP on the shells of capsids generated by DNA packaging in vivo. These capsids retain incompletely packaged DNA (ipDNA) and are called ipDNA-capsids; the ipDNA-capsids are assumed to be products of premature genome maturation-cleavage. They were isolated via preparative Nycodenz buoyant density centrifugation. For some ipDNA-capsids, Nycodenz impermeability increases hydration and generates density so low that shell hyper-expansion must exist to accommodate associated water. Electron microscopy (EM) confirmed hyper-expansion and low permeability and revealed that 3.0 mM magnesium ATP (physiological concentration) causes contraction of hyper-expanded, low-permeability ipDNA-capsids to less than mature size; 5.0 mM magnesium ATP (border of supra-physiological concentration) or more disrupts them. Additionally, excess sodium ADP reverses 3.0 mM magnesium ATP-induced contraction and re-generates hyper-expansion. The Nycodenz impermeability implies assembly perfection that suggests selection for function in DNA packaging. These findings support the above challenge and can be explained via the assumption that T3 DNA packaging includes a back-up cycle of ATP-driven capsid contraction and hyper-expansion.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA.
| | - Elena T Wright
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA.
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44
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Wang S, Zhou Z, Zhao Z, Zhang H, Haque F, Guo P. Channel of viral DNA packaging motor for real time kinetic analysis of peptide oxidation states. Biomaterials 2017; 126:10-17. [PMID: 28237908 PMCID: PMC5421631 DOI: 10.1016/j.biomaterials.2017.01.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/22/2016] [Accepted: 01/27/2017] [Indexed: 10/20/2022]
Abstract
Nanopore technology has become a powerful tool in single molecule sensing, and protein nanopores appear to be more advantageous than synthetic counterparts with regards to channel amenability, structure homogeneity, and production reproducibility. However, the diameter of most of the well-studied protein nanopores is too small to allow the passage of protein or peptides that are typically in multiple nanometers scale. The portal channel from bacteriophage SPP1 has a large channel size that allows the translocation of peptides with higher ordered structures. Utilizing single channel conductance assay and optical single molecule imaging, we observed translocation of peptides and quantitatively analyzed the dynamics of peptide oligomeric states in real-time at single molecule level. The oxidative and the reduced states of peptides were clearly differentiated based on their characteristic electronic signatures. A similar Gibbs free energy (ΔG0) was obtained when different concentrations of substrates were applied, suggesting that the use of SPP1 nanopore for real-time quantification of peptide oligomeric states is feasible. With the intrinsic nature of size and conjugation amenability, the SPP1 nanopore has the potential for development into a tool for the quantification of peptide and protein structures in real time.
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Affiliation(s)
- Shaoying Wang
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA; College of Pharmacy, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Zhi Zhou
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Zhengyi Zhao
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA; College of Pharmacy, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Hui Zhang
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Farzin Haque
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Peixuan Guo
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA.
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Abstract
Strong chain rigidity and electrostatic self-repulsion of packed double-stranded DNA in viruses require a molecular motor to pull the DNA into the capsid. However, what is the role of electrostatic interactions between different charged components in the packaging process? Though various theories and computer simulation models were developed for the understanding of viral assembly and packaging dynamics of the genome, long-range electrostatic interactions and capsid structure have typically been neglected or oversimplified. By means of molecular dynamics simulations, we explore the effects of electrostatic interactions on the packaging dynamics of DNA based on a coarse-grained DNA and capsid model by explicitly including peptide arms (PAs), linked to the inner surface of the capsid, and counterions. Our results indicate that the electrostatic interactions between PAs, DNA, and counterions have a significant influence on the packaging dynamics. We also find that the packed DNA conformations are largely affected by the structure of the PA layer, but the packaging rate is insensitive to the layer structure.
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Affiliation(s)
- Qianqian Cao
- College of Mechanical and Electrical Engineering, Jiaxing University, Jiaxing 314001, P. R. China. and Soft Matter Systems Research Group, Center for Simulational Physics, The University of Georgia, Athens, GA 30602, USA. and Institut für Theoretische Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Michael Bachmann
- Soft Matter Systems Research Group, Center for Simulational Physics, The University of Georgia, Athens, GA 30602, USA. and Instituto de Física, Universidade Federal de Mato Grosso, Cuiabá (MT), Brazil and Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte (MG), Brazil
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46
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Wechman SL, Rao XM, McMasters KM, Zhou HS. Adenovirus with DNA Packaging Gene Mutations Increased Virus Release. Viruses 2016; 8:v8120333. [PMID: 27999391 PMCID: PMC5192394 DOI: 10.3390/v8120333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/24/2016] [Accepted: 12/09/2016] [Indexed: 12/24/2022] Open
Abstract
Adenoviruses (Ads) have been extensively manipulated for the development of cancer selective replication, leading to cancer cell death or oncolysis. Clinical studies using E1-modified oncolytic Ads have shown that this therapeutic platform was safe, but with limited efficacy, indicating the necessity of targeting other viral genes for manipulation. To improve the therapeutic efficacy of oncolytic Ads, we treated the entire Ad genome repeatedly with UV-light and have isolated AdUV which efficiently lyses cancer cells as reported previously (Wechman, S. L. et al. Development of an Oncolytic Adenovirus with Enhanced Spread Ability through Repeated UV Irradiation and Cancer Selection. Viruses2016, 8, 6). In this report, we show that no mutations were observed in the early genes (E1 or E4) of AdUV while several mutations were observed within the Ad late genes which have structural or viral DNA packaging functions. This study also reported the increased release of AdUV from cancer cells. In this study, we found that AdUV inhibits tumor growth following intratumoral injection. These results indicate the potentially significant role of the viral late genes, in particular the DNA packaging genes, to enhance Ad oncolysis.
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Affiliation(s)
- Stephen L Wechman
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, USA.
- Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40202, USA.
| | - Xiao-Mei Rao
- Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40202, USA.
- James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40202, USA.
| | - Kelly M McMasters
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, USA.
- Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40202, USA.
- James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40202, USA.
| | - Heshan Sam Zhou
- Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40202, USA.
- James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40202, USA.
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY 40202, USA.
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47
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Binzel DW, Khisamutdinov E, Vieweger M, Ortega J, Li J, Guo P. Mechanism of three-component collision to produce ultrastable pRNA three-way junction of Phi29 DNA-packaging motor by kinetic assessment. RNA 2016; 22:1710-1718. [PMID: 27672132 PMCID: PMC5066623 DOI: 10.1261/rna.057646.116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/09/2016] [Indexed: 05/27/2023]
Abstract
RNA nanotechnology is rapidly emerging. Due to advantageous pharmacokinetics and favorable in vivo biodistribution, RNA nanoparticles have shown promise in targeted delivery of therapeutics. RNA nanotechnology applies bottom-up assembly, thus elucidation of the mechanism of interaction between multiple components is of fundamental importance. The tendency of diminishing concern about RNA instability has accelerated by the finding of the novel thermostable three-way junction (3WJ) motif of the phi29 DNA-packaging motor. The kinetics of these three components, each averaging 18 nucleotides (nt), was investigated to elucidate the mechanism for producing the stable 3WJ. The three fragments coassembled into the 3WJ with extraordinary speed and affinity via a two-step reaction mechanism, 3WJb + 3WJc ↔ 3WJbc + 3WJa ↔ 3WJabc The first step of reaction between 3WJb and 3WJc is highly dynamic since these two fragments only contain 8 nt for complementation. In the second step, the 3WJa, which contains 17 nt complementary to the 3WJbc complex, locks the unstable 3WJbc complex into a highly stable 3WJ. The resulting pRNA-3WJ is more stable than any of the dimer species as shown in the much more rapid association rates and slowest dissociation rate constant. The second step occurs at a very high association rate that is difficult to quantify, resulting in a rapid formation of a stable 3WJ. Elucidation of the mechanism of three-component collision in producing the ultrastable 3WJ proves a promising platform for bottom-up assembly of RNA nanoparticles as a new class of anion polymers for material science, electronic elements, or therapeutic reagents.
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Affiliation(s)
- Daniel W Binzel
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA
| | - Emil Khisamutdinov
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Mario Vieweger
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA
| | - Janice Ortega
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, Kentucky 40536, USA
| | - Jingyuan Li
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China, 1000049
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA
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48
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Kumar R, Grubmüller H. Phi29 Connector-DNA Interactions Govern DNA Crunching and Rotation, Supporting the Check-Valve Model. Biophys J 2016; 110:455-469. [PMID: 26789768 PMCID: PMC4724654 DOI: 10.1016/j.bpj.2015.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 12/08/2015] [Accepted: 12/09/2015] [Indexed: 11/28/2022] Open
Abstract
During replication of the ϕ29 bacteriophage inside a bacterial host cell, a DNA packaging motor transports the viral DNA into the procapsid against a pressure difference of up to 40 ± 20 atm. Several models have been proposed for the underlying molecular mechanism. Here we have used molecular dynamics simulations to examine the role of the connector part of the motor, and specifically the one-way revolution and the push-roll model. We have focused at the structure and intermolecular interactions between the DNA and the connector, for which a near-complete structure is available. The connector is found to induce considerable DNA deformations with respect to its canonical B-form. We further assessed by force-probe simulations to which extent the connector is able to prevent DNA leakage and found that the connector can act as a partial one-way valve by a check-valve mechanism via its mobile loops. Analysis of the geometry, flexibility, and energetics of channel lysine residues suggested that this arrangement of residues is incompatible with the observed DNA packaging step-size of ∼2.5 bp, such that the step-size is probably determined by the other components of the motor. Previously proposed DNA revolution and rolling motions inside the connector channel are both found implausible due to structural entanglement between the DNA and connector loops that have not been resolved in the crystal structure. Rather, in the simulations, the connector facilitates minor DNA rotation during the packaging process compatible with recent optical-tweezers experiments. Combined with the available experimental data, our simulation results suggest that the connector acts as a check-valve that prevents DNA leakage and induces DNA compression and rotation during DNA packaging.
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Affiliation(s)
- Rajendra Kumar
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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49
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Ji Z, Wang S, Zhao Z, Zhou Z, Haque F, Guo P. Fingerprinting of Peptides with a Large Channel of Bacteriophage Phi29 DNA Packaging Motor. Small 2016; 12:4572-8. [PMID: 27435806 PMCID: PMC5166430 DOI: 10.1002/smll.201601157] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/16/2016] [Indexed: 05/27/2023]
Abstract
Nanopore technology has become a highly sensitive and powerful tool for single molecule sensing of chemicals and biopolymers. Protein pores have the advantages of size amenability, channel homogeneity, and fabrication reproducibility. But most well-studied protein pores for sensing are too small for passage of peptide analytes that are typically a few nanometers in dimension. The funnel-shaped channel of bacteriophage phi29 DNA packaging motor has previously been inserted into a lipid membrane to serve as a larger pore with a narrowest N-terminal constriction of 3.6 nm and a wider C-terminal end of 6 nm. Here, the utility of phi29 motor channel for fingerprinting of various peptides using single molecule electrophysiological assays is reported. The translocation of peptides is proved unequivocally by single molecule fluorescence imaging. Current blockage percentage and distinctive current signatures are used to distinguish peptides with high confidence. Each peptide generated one or two distinct current blockage peaks, serving as typical fingerprint for each peptide. The oligomeric states of peptides can also be studied in real time at single molecule level. The results demonstrate the potential for further development of phi29 motor channel for detection of disease-associated peptide biomarkers.
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50
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Moon BY, Park JY, Robinson DA, Thomas JC, Park YH, Thornton JA, Seo KS. Mobilization of Genomic Islands of Staphylococcus aureus by Temperate Bacteriophage. PLoS One 2016; 11:e0151409. [PMID: 26953931 PMCID: PMC4783081 DOI: 10.1371/journal.pone.0151409] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/26/2016] [Indexed: 01/21/2023] Open
Abstract
The virulence of Staphylococcus aureus, in both human and animal hosts, is largely influenced by the acquisition of mobile genetic elements (MGEs). Most S. aureus strains carry a variety of MGEs, including three genomic islands (νSaα, νSaβ, νSaγ) that are diverse in virulence gene content but conserved within strain lineages. Although the mobilization of pathogenicity islands, phages and plasmids has been well studied, the mobilization of genomic islands is poorly understood. We previously demonstrated the mobilization of νSaβ by the adjacent temperate bacteriophage ϕSaBov from strain RF122. In this study, we demonstrate that ϕSaBov mediates the mobilization of νSaα and νSaγ, which are located remotely from ϕSaBov, mostly to recipient strains belonging to ST151. Phage DNA sequence analysis revealed that chromosomal DNA excision events from RF122 were highly specific to MGEs, suggesting sequence-specific DNA excision and packaging events rather than generalized transduction by a temperate phage. Disruption of the int gene in ϕSaBov did not affect phage DNA excision, packaging, and integration events. However, disruption of the terL gene completely abolished phage DNA packing events, suggesting that the primary function of temperate phage in the transfer of genomic islands is to allow for phage DNA packaging by TerL and that transducing phage particles are the actual vehicle for transfer. These results extend our understanding of the important role of bacteriophage in the horizontal transfer and evolution of genomic islands in S. aureus.
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Affiliation(s)
- Bo Youn Moon
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, United States of America
- Department of Microbiology, College of Veterinary Medicine and BK21 Program for Veterinary Science, Seoul National University, Seoul, 151–742, South Korea
| | - Joo Youn Park
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, United States of America
| | - D. Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS 39216, United States of America
| | - Jonathan C. Thomas
- Department of Biology, University of Bolton, Bolton, Greater Manchester, BL3 5AB United Kingdom
| | - Yong Ho Park
- Department of Microbiology, College of Veterinary Medicine and BK21 Program for Veterinary Science, Seoul National University, Seoul, 151–742, South Korea
| | - Justin A. Thornton
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, United States of America
| | - Keun Seok Seo
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, United States of America
- * E-mail:
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