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Takemata N. How Do Thermophiles Organize Their Genomes? Microbes Environ 2024; 39:n/a. [PMID: 38839371 DOI: 10.1264/jsme2.me23087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
All cells must maintain the structural and functional integrity of the genome under a wide range of environments. High temperatures pose a formidable challenge to cells by denaturing the DNA double helix, causing chemical damage to DNA, and increasing the random thermal motion of chromosomes. Thermophiles, predominantly classified as bacteria or archaea, exhibit an exceptional capacity to mitigate these detrimental effects and prosper under extreme thermal conditions, with some species tolerating temperatures higher than 100°C. Their genomes are mainly characterized by the presence of reverse gyrase, a unique topoisomerase that introduces positive supercoils into DNA. This enzyme has been suggested to maintain the genome integrity of thermophiles by limiting DNA melting and mediating DNA repair. Previous studies provided significant insights into the mechanisms by which NAPs, histones, SMC superfamily proteins, and polyamines affect the 3D genomes of thermophiles across different scales. Here, I discuss current knowledge of the genome organization in thermophiles and pertinent research questions for future investigations.
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Affiliation(s)
- Naomichi Takemata
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
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2
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K G, Thomas AR, T SV, Mandal SS. Structural and thermodynamic insights into the Cren7 mediated DNA organization in Crenarchaeota. Phys Chem Chem Phys 2022; 24:19401-19413. [DOI: 10.1039/d2cp02190k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Archaea have histone homologues and chromatin proteins to organize their DNA into a compact form and allow them to survive in extreme climatic conditions. Cren7 is one such chromatin protein...
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Rocha MS, Storm IM, Bazoni RF, Ramos ÉB, Hernandez-Garcia A, Cohen Stuart MA, Leermakers F, de Vries R. Force and Scale Dependence of the Elasticity of Self-Assembled DNA Bottle Brushes. Macromolecules 2018; 51:204-212. [PMID: 29339838 PMCID: PMC5763285 DOI: 10.1021/acs.macromol.7b01795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 12/13/2017] [Indexed: 11/30/2022]
Abstract
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As a model system
to study the elasticity of bottle-brush polymers,
we here introduce self-assembled DNA bottle brushes, consisting of
a DNA main chain that can be very long and still of precisely defined
length, and precisely monodisperse polypeptide side chains that are
physically bound to the DNA main chains. Polypeptide side chains have
a diblock architecture, where one block is a small archaeal nucleoid
protein Sso7d that strongly binds to DNA. The other block is a net
neutral, hydrophilic random coil polypeptide with a length of exactly
798 amino acids. Light scattering shows that for saturated brushes
the grafting density is one side chain per 5.6 nm of DNA main chain.
According to small-angle X-ray scattering, the brush diameter is D = 17 nm. By analyzing configurations of adsorbed DNA bottle
brushes using AFM, we find that the effective persistence of the saturated
DNA bottle brushes is Peff = 95 nm, but
from force–extension curves of single DNA bottle brushes measured
using optical tweezers we find Peff =
15 nm. The latter is equal to the value expected for DNA coated by
the Sso7d binding block alone. The apparent discrepancy between the
two measurements is rationalized in terms of the scale dependence
of the bottle-brush elasticity using theory previously developed to
analyze the scale-dependent electrostatic stiffening of DNA at low
ionic strengths.
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Affiliation(s)
- Márcio Santos Rocha
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa Viçosa, Minas Gerais, Brazil
| | - Ingeborg M Storm
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Raniella Falchetto Bazoni
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa Viçosa, Minas Gerais, Brazil
| | - Ésio Bessa Ramos
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa Viçosa, Minas Gerais, Brazil
| | - Armando Hernandez-Garcia
- Departamento de Química de Biomacromoleculas, Instituto de Química, Universidad Nacional Autónoma de México, México City, México
| | - Martien A Cohen Stuart
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Frans Leermakers
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Hernandez-Garcia A, Estrich NA, Werten MWT, Van Der Maarel JRC, LaBean TH, de Wolf FA, Cohen Stuart MA, de Vries R. Precise Coating of a Wide Range of DNA Templates by a Protein Polymer with a DNA Binding Domain. ACS NANO 2017; 11:144-152. [PMID: 27936577 DOI: 10.1021/acsnano.6b05938] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Emerging DNA-based nanotechnologies would benefit from the ability to modulate the properties (e.g., solubility, melting temperature, chemical stability) of diverse DNA templates (single molecules or origami nanostructures) through controlled, self-assembling coatings. We here introduce a DNA coating agent, called C8-BSso7d, which binds to and coats with high specificity and affinity, individual DNA molecules as well as folded origami nanostructures. C8-BSso7d coats and protects without condensing, collapsing or destroying the spatial structure of the underlying DNA template. C8-BSso7d combines the specific nonelectrostatic DNA binding affinity of an archeal-derived DNA binding domain (Sso7d, 7 kDa) with a long hydrophilic random coil polypeptide (C8, 73 kDa), which provides colloidal stability (solubility) through formation of polymer brushes around the DNA templates. C8-BSso7d is produced recombinantly in yeast and has a precise (but engineerable) amino acid sequence of precise length. Using electrophoresis, AFM, and fluorescence microscopy we demonstrate protein coat formation with stiffening of one-dimensional templates (linear dsDNA, supercoiled dsDNA and circular ssDNA), as well as coat formation without any structural distortion or disruption of two-dimensional DNA origami template. Combining the programmability of DNA with the nonperturbing precise coating capability of the engineered protein C8-BSso7d holds promise for future applications such as the creation of DNA-protein hybrid networks, or the efficient transfection of individual DNA nanostructures into cells.
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Affiliation(s)
- Armando Hernandez-Garcia
- Physical Chemistry and Soft Matter, Wageningen University and Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Nicole A Estrich
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Marc W T Werten
- Wageningen UR Food and Biobased Research, Wageningen University and Research , Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | | | - Thomas H LaBean
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Frits A de Wolf
- Wageningen UR Food and Biobased Research, Wageningen University and Research , Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Martien A Cohen Stuart
- Physical Chemistry and Soft Matter, Wageningen University and Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University and Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Peeters E, Driessen RPC, Werner F, Dame RT. The interplay between nucleoid organization and transcription in archaeal genomes. Nat Rev Microbiol 2015; 13:333-41. [PMID: 25944489 DOI: 10.1038/nrmicro3467] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The archaeal genome is organized by either eukaryotic-like histone proteins or bacterial-like nucleoid-associated proteins. Recent studies have revealed novel insights into chromatin dynamics and their effect on gene expression in archaeal model organisms. In this Progress article, we discuss the interplay between chromatin proteins, such as histones and Alba, and components of the basal transcription machinery, as well as between chromatin structure and gene-specific transcription factors in archaea. Such an interplay suggests that chromatin might have a role in regulating gene expression on both a global and a gene-specific level. Moreover, several archaeal transcription factors combine a global gene regulatory role with an architectural role, thus contributing to chromatin organization and compaction, as well as gene expression. We describe the emerging principles underlying how these factors cooperate in nucleoid structuring and gene regulation.
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Affiliation(s)
- Eveline Peeters
- 1] Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium. [2]
| | - Rosalie P C Driessen
- 1] Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands. [2]
| | - Finn Werner
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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Črnigoj M, Podlesek Z, Zorko M, Jerala R, Anderluh G, Ulrih NP. Interactions of archaeal chromatin proteins Alba1 and Alba2 with nucleic acids. PLoS One 2013; 8:e58237. [PMID: 23469156 PMCID: PMC3585288 DOI: 10.1371/journal.pone.0058237] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 02/01/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Architectural proteins have important roles in compacting and organising chromosomal DNA. There are two potential histone counterpart peptide sequences (Alba1 and Alba2) in the Aeropyrum pernix genome (APE1832.1 and APE1823). METHODOLOGY/PRINCIPAL FINDINGS THESE TWO PEPTIDES WERE EXPRESSED AND THEIR INTERACTIONS WITH VARIOUS DNAS WERE STUDIED USING A COMBINATION OF VARIOUS EXPERIMENTAL TECHNIQUES: surface plasmon resonance, UV spectrophotometry, circular dichroism-spectropolarimetry, gel-shift assays, and isothermal titration calorimetry. CONCLUSIONS/SIGNIFICANCE Our data indicate that there are significant differences in the properties of the Alba1 and Alba2 proteins. Both of these Alba proteins can thermally stabilise DNA polynucleotides, as seen from UV melting curves. Alba2 and equimolar mixtures of Alba1/Alba2 have greater effects on the thermal stability of poly(dA-dT).poly(dA-dT). Surface plasmon resonance sensorgrams for binding of Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 to DNA oligonucleotides show different binding patterns. Circular dichroism indicates that Alba2 has a less-ordered secondary structure than Alba1. The secondary structures of the Alba proteins are not significantly influenced by DNA binding, even at high temperatures. Based on these data, we conclude that Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 show different properties in their binding to various DNAs.
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Affiliation(s)
- Miha Črnigoj
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Zdravko Podlesek
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Mateja Zorko
- National Chemical Institute of Slovenia, Ljubljana, Slovenia
| | - Roman Jerala
- National Chemical Institute of Slovenia, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
- Centre of Excellence EN-FIST, Ljubljana, Slovenia
| | - Gregor Anderluh
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- National Chemical Institute of Slovenia, Ljubljana, Slovenia
| | - Nataša Poklar Ulrih
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CipKeBiP), Ljubljana, Slovenia
- * E-mail:
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Chen L, Zheng QC, Yu LY, Chu WT, Zhang JL, Xue Q, Zhang HX, Sun CC. Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis. J Biomol Struct Dyn 2012; 30:716-27. [PMID: 22731116 DOI: 10.1080/07391102.2012.689702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the assembly of DNA-protein complex, the DNA kinking plays an important role in nucleoprotein structures and gene regulation. Molecular dynamics (MD) simulations were performed on specific protein-DNA complexes in this study to investigate the stability and structural transitions of DNA depending on temperature. Furthermore, we introduced the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) approach to analyze the interactions between DNA and protein in hyperthermophile. Focused on two specific Sso7d-DNA complexes (PDB codes: 1BNZ and 1BF4), we performed MD simulations at four temperatures (300, 360, 420, and 480 K) and MM-PBSA at 300 and 360 K to illustrate detailed information on the changes of DNA. Our results show that Sso7d stabilizes DNA duplex over a certain temperature range and DNA molecules undergo B-like to A-like form transitions in the binary complex with the temperature increasing, which are consistent with the experimental data. Our work will contribute to a better understanding of protein-DNA interaction.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, P.R. China
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Zhang Z, Guo L, Huang L. Archaeal chromatin proteins. SCIENCE CHINA-LIFE SCIENCES 2012; 55:377-85. [PMID: 22645082 DOI: 10.1007/s11427-012-4322-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 04/17/2012] [Indexed: 10/28/2022]
Abstract
Archaea, along with Bacteria and Eukarya, are the three domains of life. In all living cells, chromatin proteins serve a crucial role in maintaining the integrity of the structure and function of the genome. An array of small, abundant and basic DNA-binding proteins, considered candidates for chromatin proteins, has been isolated from the Euryarchaeota and the Crenarchaeota, the two major phyla in Archaea. While most euryarchaea encode proteins resembling eukaryotic histones, crenarchaea appear to synthesize a number of unique DNA-binding proteins likely involved in chromosomal organization. Several of these proteins (e.g., archaeal histones, Sac10b homologs, Sul7d, Cren7, CC1, etc.) have been extensively studied. However, whether they are chromatin proteins and how they function in vivo remain to be fully understood. Future investigation of archaeal chromatin proteins will lead to a better understanding of chromosomal organization and gene expression in Archaea and provide valuable information on the evolution of DNA packaging in cellular life.
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Affiliation(s)
- ZhenFeng Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Abstract
Architectural proteins play an important role in compacting and organizing the chromosomal DNA in all three kingdoms of life (Eukarya, Bacteria and Archaea). These proteins are generally not conserved at the amino acid sequence level, but the mechanisms by which they modulate the genome do seem to be functionally conserved across kingdoms. On a generic level, architectural proteins can be classified based on their structural effect as DNA benders, DNA bridgers or DNA wrappers. Although chromatin organization in archaea has not been studied extensively, quite a number of architectural proteins have been identified. In the present paper, we summarize the knowledge currently available on these proteins in Crenarchaea. By the type of architectural proteins available, the crenarchaeal nucleoid shows similarities with that of Bacteria. It relies on the action of a large set of small, abundant and generally basic proteins to compact and organize their genome and to modulate its activity.
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