1
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Banerjee T, Geethika K, Kanbayashi S, Takahashi S, Mandal SS, Kamagata K. Thermostable Nucleoid Protein Cren7 Slides Along DNA and Rapidly Dissociates From DNA While Not Inhibiting the Sliding of Other DNA-binding Protein. J Mol Biol 2024; 436:168803. [PMID: 39326492 DOI: 10.1016/j.jmb.2024.168803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 09/17/2024] [Accepted: 09/19/2024] [Indexed: 09/28/2024]
Abstract
A nucleoid protein Cren7 compacts DNA, contributing to the living of Crenarchaeum in high temperature environment. In this study, we investigated the dynamic behavior of Cren7 on DNA and its functional relation using single-molecule fluorescence microscopy. We found two mobility modes of Cren7, sliding along DNA and pausing on it, and the rapid dissociation kinetics from DNA. The salt dependence analysis suggests a sliding with continuous contact to DNA, rather than hopping/jumping. The mutational analysis demonstrates that Cren7 slides along DNA while Trp (W26) residue interacts with the DNA. Furthermore, Cren7 does not impede the target search by a model transcription factor p53, implying no significant interference to other DNA-binding proteins on DNA. At high concentration of Cren7, the molecules form large clusters on DNA via bridging, which compacts DNA. We discuss how the dynamic behavior of Cren7 on DNA enables DNA-compaction and protein-bypass functions.
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Affiliation(s)
- Trishit Banerjee
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - K Geethika
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
| | - Saori Kanbayashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Soumit S Mandal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India; Center for Atomic, Molecular and Optical Sciences & Technologies, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India.
| | - Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan; Faculty of Engineering and Graduate School of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan.
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2
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Hu Y, Schwab S, Deiss S, Escudeiro P, van Heesch T, Joiner J, Vreede J, Hartmann M, Lupas A, Alvarez B, Alva V, Dame R. Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending. Nucleic Acids Res 2024; 52:8193-8204. [PMID: 38864377 PMCID: PMC11317129 DOI: 10.1093/nar/gkae485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 05/01/2024] [Accepted: 05/24/2024] [Indexed: 06/13/2024] Open
Abstract
Histones are essential for genome compaction and transcription regulation in eukaryotes, where they assemble into octamers to form the nucleosome core. In contrast, archaeal histones assemble into dimers that form hypernucleosomes upon DNA binding. Although histone homologs have been identified in bacteria recently, their DNA-binding characteristics remain largely unexplored. Our study reveals that the bacterial histone HBb (Bd0055) is indispensable for the survival of Bdellovibrio bacteriovorus, suggesting critical roles in DNA organization and gene regulation. By determining crystal structures of free and DNA-bound HBb, we unveil its distinctive dimeric assembly, diverging from those of eukaryotic and archaeal histones, while also elucidating how it binds and bends DNA through interaction interfaces reminiscent of eukaryotic and archaeal histones. Building on this, by employing various biophysical and biochemical approaches, we further substantiated the ability of HBb to bind and compact DNA by bending in a sequence-independent manner. Finally, using DNA affinity purification and sequencing, we reveal that HBb binds along the entire genomic DNA of B. bacteriovorus without sequence specificity. These distinct DNA-binding properties of bacterial histones, showcasing remarkable similarities yet significant differences from their archaeal and eukaryotic counterparts, highlight the diverse roles histones play in DNA organization across all domains of life.
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Affiliation(s)
- Yimin Hu
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Samuel Schwab
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands; Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Silvia Deiss
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Pedro Escudeiro
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Thor van Heesch
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, The Netherlands
| | - Joe D Joiner
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Jocelyne Vreede
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, The Netherlands
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Birte Hernandez Alvarez
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands; Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
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3
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Blombach F, Sýkora M, Case J, Feng X, Baquero DP, Fouqueau T, Phung DK, Barker D, Krupovic M, She Q, Werner F. Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays. Nat Commun 2024; 15:1620. [PMID: 38388540 PMCID: PMC10883916 DOI: 10.1038/s41467-024-45728-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Abstract
CRISPR arrays form the physical memory of CRISPR adaptive immune systems by incorporating foreign DNA as spacers that are often AT-rich and derived from viruses. As promoter elements such as the TATA-box are AT-rich, CRISPR arrays are prone to harbouring cryptic promoters. Sulfolobales harbour extremely long CRISPR arrays spanning several kilobases, a feature that is accompanied by the CRISPR-specific transcription factor Cbp1. Aberrant Cbp1 expression modulates CRISPR array transcription, but the molecular mechanisms underlying this regulation are unknown. Here, we characterise the genome-wide Cbp1 binding at nucleotide resolution and characterise the binding motifs on distinct CRISPR arrays, as well as on unexpected non-canonical binding sites associated with transposons. Cbp1 recruits Cren7 forming together 'chimeric' chromatin-like structures at CRISPR arrays. We dissect Cbp1 function in vitro and in vivo and show that the third helix-turn-helix domain is responsible for Cren7 recruitment, and that Cbp1-Cren7 chromatinization plays a dual role in the transcription of CRISPR arrays. It suppresses spurious transcription from cryptic promoters within CRISPR arrays but enhances CRISPR RNA transcription directed from their cognate promoters in their leader region. Our results show that Cbp1-Cren7 chromatinization drives the productive expression of long CRISPR arrays.
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Affiliation(s)
- Fabian Blombach
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
| | - Michal Sýkora
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Jo Case
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Xu Feng
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute, Shandong University, Qingdao, 266237, PR China
| | - Diana P Baquero
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, F-75015, Paris, France
| | - Thomas Fouqueau
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Duy Khanh Phung
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Declan Barker
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, F-75015, Paris, France
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute, Shandong University, Qingdao, 266237, PR China
| | - Finn Werner
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
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4
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van der Valk RA, Zarguit I, Laurens N, Dame RT. Tethered Particle Motion Analysis of DNA-Binding Properties of Architectural Proteins. Methods Mol Biol 2024; 2819:477-496. [PMID: 39028520 DOI: 10.1007/978-1-0716-3930-6_22] [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: 07/20/2024]
Abstract
Architectural DNA-binding proteins are key to the organization and compaction of genomic DNA inside cells. Tethered particle motion (TPM) permits analysis of DNA conformation and detection of changes in conformation induced by such proteins at the single molecule level in vitro. As many individual protein-DNA complexes can be investigated in parallel, these experiments have high throughput. TPM is therefore well suited for characterization of the effects of protein-DNA stoichiometry and changes in physicochemical conditions (pH, osmolarity, and temperature). Here, we describe in detail how to perform tethered particle motion experiments on complexes between DNA and architectural proteins to determine their structural and biochemical characteristics.
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Affiliation(s)
| | - Ilias Zarguit
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Niels Laurens
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
- Faculty Governance and Global Affairs, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
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5
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K G, Verma A, Mondal P, Mandal SS. Molecular contacts in the Cren7-DNA complex: A quantitative investigation for electrostatic interaction. Biophys J 2023; 122:1701-1719. [PMID: 37016575 PMCID: PMC10183371 DOI: 10.1016/j.bpj.2023.03.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/15/2023] [Accepted: 03/29/2023] [Indexed: 04/06/2023] Open
Abstract
The molecular association of proteins with nucleic acids leading to the formation of macromolecular complexes is a crucial step in several biological processes. Stabilization of these complexes involves electrostatic interactions between ion pairs (salt bridges) of nucleic acid phosphates and protein side chains. The crenarchaeal DNA binding protein, Cren7 plays a key role in the regulation of chromosomal structure and gene expression in eukaryotic extremophiles. However, the molecular contacts that occur at the interface of protein-DNA complexes and their contribution to the electrostatic interaction have not been fully elucidated. This work presents a quantitative description of the mechanism of the electrostatic interaction between the protein and DNA. We have identified a few residues located at the Cren7-DNA interface that could potentially be responsible for the interaction. Structural studies using circular dichroism indicate mutation of these surface residues minimally affect their structure and stability. The binding affinity of these mutants for the DNA duplexes was examined from reverse titration, biolayer interferometry, and fluorescence anisotropy measurements with calf thymus DNA, polynucleotides, and small DNA oligonucleotides. The resulting kinetic parameters highlight a difference in electrostatic interactions potentials exhibited by residues positioned at different locations of the protein-DNA interface. Computational studies attribute this difference to their surrounding atmosphere and energetic stabilization parameters. The biophysical approach described here can be extended for other proteins that play a crucial role in DNA bending and compaction, to properly evaluate the role of specific residues on the mechanisms of DNA binding.
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Affiliation(s)
- Geethika K
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, India
| | - Arunima Verma
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, India
| | - Padmabati Mondal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, India.
| | - Soumit S Mandal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, India.
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6
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Essentiality of core hydrophobicity to the structure and function of archaeal chromatin protein Cren7. Int J Biol Macromol 2022; 214:381-390. [PMID: 35728637 DOI: 10.1016/j.ijbiomac.2022.06.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 04/29/2022] [Accepted: 06/14/2022] [Indexed: 11/23/2022]
Abstract
Studies on the structure-function relationship of protein greatly help to understand not only the principles of protein folding but also the rationales of protein engineering. Crenarchaeal chromatin protein Cren7 provides an excellent research model for this issue. The small protein adopts a 'β-barrel' fold, formed by the double-stranded antiparallel β-sheet 1 tightly packing with the triple-stranded antiparallel β-sheet 2. The simple structure of Cren7 is stabilized by the hydrophobic core between the β-sheets, consisting of the side chains of V8, V10, L20, V25, F41 and F50. In the present work, mutation analyses by alanine substitution of each of the residues in the hydrophobic core were performed. Circular dichroism spectra and nuclear magnetic resonance analyses showed that mutation of F41 led to a significant misfolding of Cren7 through disruption of the β-sheets. Meanwhile, the mutant F41A showed a reduced thermostatility (Tm of 53.2 °C), as compared with the wild-type Cren7 (Tm > 80 °C). Biolayer interferometry and nick-closure assays showed the largely unchanged activities in DNA binding and supercoiling of F41A, indicating the DNA interface of Cren7 was generally retained in F41A. However, F41A was unable to mediate DNA bridging, probably due to the impairment in forming oligomers/polymers on DNA. Atomic force microscopic images of the F41A-DNA complexes also revealed that F41A nearly completely lost the ability to compact DNA into highly condensed structures. Our results not only reveal the critical role of F41 in protein folding of Cren7 but also provide new insights into the structure-function relationships of thermostable proteins.
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7
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DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius. Biomolecules 2022; 12:biom12040524. [PMID: 35454113 PMCID: PMC9025068 DOI: 10.3390/biom12040524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 02/06/2023] Open
Abstract
In archaeal microorganisms, the compaction and organization of the chromosome into a dynamic but condensed structure is mediated by diverse chromatin-organizing proteins in a lineage-specific manner. While many archaea employ eukaryotic-type histones for nucleoid organization, this is not the case for the crenarchaeal model species Sulfolobus acidocaldarius and related species in Sulfolobales, in which the organization appears to be mostly reliant on the action of small basic DNA-binding proteins. There is still a lack of a full understanding of the involved proteins and their functioning. Here, a combination of in vitro and in vivo methodologies is used to study the DNA-binding properties of Sul12a, an uncharacterized small basic protein conserved in several Sulfolobales species displaying a winged helix–turn–helix structural motif and annotated as a transcription factor. Genome-wide chromatin immunoprecipitation and target-specific electrophoretic mobility shift assays demonstrate that Sul12a of S. acidocaldarius interacts with DNA in a non-sequence specific manner, while atomic force microscopy imaging of Sul12a–DNA complexes indicate that the protein induces structural effects on the DNA template. Based on these results, and a contrario to its initial annotation, it can be concluded that Sul12a is a novel chromatin-organizing protein.
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8
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Cajili MKM, Prieto EI. Interplay between Alba and Cren7 Regulates Chromatin Compaction in Sulfolobus solfataricus. Biomolecules 2022; 12:biom12040481. [PMID: 35454068 PMCID: PMC9030869 DOI: 10.3390/biom12040481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/03/2022] [Accepted: 03/15/2022] [Indexed: 01/06/2023] Open
Abstract
Chromatin compaction and regulation are essential processes for the normal function of all organisms, yet knowledge on how archaeal chromosomes are packed into higher-order structures inside the cell remains elusive. In this study, we investigated the role of archaeal architectural proteins Alba and Cren7 in chromatin folding and dynamics. Atomic force microscopy revealed that Sulfolobus solfataricus chromatin is composed of 28 nm fibers and 60 nm globular structures. In vitro reconstitution showed that Alba can mediate the formation of folded DNA structures in a concentration-dependent manner. Notably, it was demonstrated that Alba on its own can form higher-order structures with DNA. Meanwhile, Cren7 was observed to affect the formation of Alba-mediated higher-order chromatin structures. Overall, the results suggest an interplay between Alba and Cren7 in regulating chromatin compaction in archaea.
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9
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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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10
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Henneman B, Brouwer TB, Erkelens AM, Kuijntjes GJ, van Emmerik C, van der Valk RA, Timmer M, Kirolos NCS, van Ingen H, van Noort J, Dame RT. Mechanical and structural properties of archaeal hypernucleosomes. Nucleic Acids Res 2021; 49:4338-4349. [PMID: 33341892 PMCID: PMC8096283 DOI: 10.1093/nar/gkaa1196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 11/13/2020] [Accepted: 11/23/2020] [Indexed: 11/21/2022] Open
Abstract
Many archaea express histones, which organize the genome and play a key role in gene regulation. The structure and function of archaeal histone–DNA complexes remain however largely unclear. Recent studies show formation of hypernucleosomes consisting of DNA wrapped around an ‘endless’ histone-protein core. However, if and how such a hypernucleosome structure assembles on a long DNA substrate and which interactions provide for its stability, remains unclear. Here, we describe micromanipulation studies of complexes of the histones HMfA and HMfB with DNA. Our experiments show hypernucleosome assembly which results from cooperative binding of histones to DNA, facilitated by weak stacking interactions between neighboring histone dimers. Furthermore, rotational force spectroscopy demonstrates that the HMfB–DNA complex has a left-handed chirality, but that torque can drive it in a right-handed conformation. The structure of the hypernucleosome thus depends on stacking interactions, torque, and force. In vivo, such modulation of the archaeal hypernucleosome structure may play an important role in transcription regulation in response to environmental changes.
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Affiliation(s)
- Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Thomas B Brouwer
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333CA Leiden, The Netherlands
| | - Amanda M Erkelens
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Gert-Jan Kuijntjes
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333CA Leiden, The Netherlands
| | - Clara van Emmerik
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Ramon A van der Valk
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Monika Timmer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Nancy C S Kirolos
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Hugo van Ingen
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - John van Noort
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333CA Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
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11
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Park G, Cho MK, Jung Y. Sequence-Dependent Kink Formation in Short DNA Loops: Theory and Molecular Dynamics Simulations. J Chem Theory Comput 2021; 17:1308-1317. [PMID: 33570937 DOI: 10.1021/acs.jctc.0c01116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Kink formation is essential in highly bent DNA complexed with gene regulatory proteins such as histones to release the bending stress stored within the DNA duplex. Local opening of the double-stranded DNA creates a sharp turn along the specific sequence, which leads to the global bending of the DNA strand. Despite the critical role of kink formation, it is still challenging to predict the position of kink formation for a given DNA sequence. In this study, we propose a theoretical model and perform molecular dynamics simulations to quantify the sequence-dependent kink probability of a strongly bent DNA. By incorporating the elastic bending energy and the sequence-specific thermodynamic parameters, we investigate the importance of the DNA sequence on kink formation. We find that the sequence with TA dinucleotide repeats flanked by GC steps increases the kink propensity by more than an order of magnitude under the same bending stress. The number of base pairs involved in the local opening is found to be coupled with the sequence-specific bubble formation free energy. Our study elucidates the molecular origin of the sequence heterogeneity on kink formation, which is fundamental to understanding protein-DNA recognition.
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Affiliation(s)
- Gyehyun Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Myung Keun Cho
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - YounJoon Jung
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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12
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Laursen SP, Bowerman S, Luger K. Archaea: The Final Frontier of Chromatin. J Mol Biol 2020; 433:166791. [PMID: 33383035 PMCID: PMC7987875 DOI: 10.1016/j.jmb.2020.166791] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 12/26/2022]
Abstract
The three domains of life employ various strategies to organize their genomes. Archaea utilize features similar to those found in both eukaryotic and bacterial chromatin to organize their DNA. In this review, we discuss the current state of research regarding the structure-function relationships of several archaeal chromatin proteins (histones, Alba, Cren7, and Sul7d). We address individual structures as well as inferred models for higher-order chromatin formation. Each protein introduces a unique phenotype to chromatin organization, and these structures are put into the context of in vivo and in vitro data. We close by discussing the present gaps in knowledge that are preventing further studies of the organization of archaeal chromatin, on both the organismal and domain level.
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Affiliation(s)
- Shawn P Laursen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, United States
| | - Samuel Bowerman
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, United States
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, United States; Howard Hughes Medical Institute, Chevy Chase, MD 20815, United States.
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13
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Wenck BR, Santangelo TJ. Archaeal transcription. Transcription 2020; 11:199-210. [PMID: 33112729 PMCID: PMC7714419 DOI: 10.1080/21541264.2020.1838865] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
Increasingly sophisticated biochemical and genetic techniques are unraveling the regulatory factors and mechanisms that control gene expression in the Archaea. While some similarities in regulatory strategies are universal, archaeal-specific regulatory strategies are emerging to complement a complex patchwork of shared archaeal-bacterial and archaeal-eukaryotic regulatory mechanisms employed in the archaeal domain. The prokaryotic archaea encode core transcription components with homology to the eukaryotic transcription apparatus and also share a simplified eukaryotic-like initiation mechanism, but also deploy tactics common to bacterial systems to regulate promoter usage and influence elongation-termination decisions. We review the recently established complete archaeal transcription cycle, highlight recent findings of the archaeal transcription community and detail the expanding post-initiation regulation imposed on archaeal transcription.
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Affiliation(s)
- Breanna R. Wenck
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Thomas J. Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
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14
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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: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [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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15
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Abstract
Over the past decade, advances in methodologies for the determination of chromosome conformation have provided remarkable insight into the local and higher-order organization of bacterial and eukaryotic chromosomes. Locally folded domains are found in both bacterial and eukaryotic genomes, although they vary in size. Importantly, genomes of metazoans also possess higher-order organization into A- and B-type compartments, regions of transcriptionally active and inactive chromatin, respectively. Until recently, nothing was known about the organization of genomes of organisms in the third domain of life - the archaea. However, despite archaea possessing simple circular genomes that are morphologically reminiscent of those seen in many bacteria, a recent study of archaea of the genus Sulfolobus has revealed that it organizes its genome into large-scale domains. These domains further interact to form defined A- and B-type compartments. The interplay of transcription and localization of a novel structural maintenance of chromosomes (SMC) superfamily protein, termed coalescin, defines compartment identity. In this Review, we discuss the mechanistic and evolutionary implications of these findings.
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Affiliation(s)
- Naomichi Takemata
- Biology Department, Indiana University, Bloomington, USA.,Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, USA
| | - Stephen D Bell
- Biology Department, Indiana University, Bloomington, USA .,Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, USA
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16
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17
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Sanders TJ, Marshall CJ, Santangelo TJ. The Role of Archaeal Chromatin in Transcription. J Mol Biol 2019; 431:4103-4115. [PMID: 31082442 PMCID: PMC6842674 DOI: 10.1016/j.jmb.2019.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/02/2019] [Accepted: 05/04/2019] [Indexed: 02/08/2023]
Abstract
Genomic organization impacts accessibility and movement of information processing systems along DNA. DNA-bound proteins dynamically dictate gene expression and provide regulatory potential to tune transcription rates to match ever-changing environmental conditions. Archaeal genomes are typically small, circular, gene dense, and organized either by histone proteins that are homologous to their eukaryotic counterparts, or small basic proteins that function analogously to bacterial nucleoid proteins. We review here how archaeal genomes are organized and how such organization impacts archaeal gene expression, focusing on conserved DNA-binding proteins within the clade and the factors that are known to impact transcription initiation and elongation within protein-bound genomes.
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Affiliation(s)
- Travis J Sanders
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Craig J Marshall
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
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18
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Sun M, Feng X, Liu Z, Han W, Liang YX, She Q. An Orc1/Cdc6 ortholog functions as a key regulator in the DNA damage response in Archaea. Nucleic Acids Res 2019; 46:6697-6711. [PMID: 29878182 PMCID: PMC6061795 DOI: 10.1093/nar/gky487] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 05/17/2018] [Indexed: 12/04/2022] Open
Abstract
While bacteria and eukaryotes show distinct mechanisms of DNA damage response (DDR) regulation, investigation of ultraviolet (UV)-responsive expression in a few archaea did not yield any conclusive evidence for an archaeal DDR regulatory network. Nevertheless, expression of Orc1-2, an ortholog of the archaeal origin recognition complex 1/cell division control protein 6 (Orc1/Cdc6) superfamily proteins was strongly activated in Sulfolobus solfataricus and Sulfolobus acidocaldarius upon UV irradiation. Here, a series of experiments were conducted to investigate the possible functions of Orc1-2 in DNA damage repair in Sulfolobus islandicus. Study of DDR in Δorc1-2 revealed that Orc1-2 deficiency abolishes DNA damage-induced differential expression of a large number of genes and the mutant showed hypersensitivity to DNA damage treatment. Reporter gene and DNase I footprinting assays demonstrated that Orc1-2 interacts with a conserved hexanucleotide motif present in several DDR gene promoters and regulates their expression. Manipulation of orc1-2 expression by promoter substitution in this archaeon revealed that a high level of orc1-2 expression is essential but not sufficient to trigger DDR. Together, these results have placed Orc1-2 in the heart of the archaeal DDR regulation, and the resulting Orc1-2-centered regulatory circuit represents the first DDR network identified in Archaea, the third domain of life.
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Affiliation(s)
- Mengmeng Sun
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China.,Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Xu Feng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China.,Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Zhenzhen Liu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Wenyuan Han
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Yun Xiang Liang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qunxin She
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China.,Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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19
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Zhang Z, Zhao M, Chen Y, Wang L, Liu Q, Dong Y, Gong Y, Huang L. Architectural roles of Cren7 in folding crenarchaeal chromatin filament. Mol Microbiol 2019; 111:556-569. [PMID: 30499242 DOI: 10.1111/mmi.14173] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2018] [Indexed: 01/01/2023]
Abstract
Archaea have evolved various strategies in chromosomal organization. While histone homologues exist in most archaeal phyla, Cren7 is a chromatin protein conserved in the Crenarchaeota. Here, we show that Cren7 preferentially binds DNA with AT-rich sequences over that with GC-rich sequences with a binding size of 6~7 bp. Structural studies of Cren7 in complex with either an 18-bp or a 20-bp double-stranded DNA fragment reveal that Cren7 binds to the minor groove of DNA as monomers in a head-to-tail manner. The neighboring Cren7 monomers are located on the opposite sides of the DNA duplex, with each introducing a single-step sharp kink by intercalation of the hydrophobic side chain of Leu28, bending the DNA into an S-shape conformation. A structural model for the chromatin fiber folded by Cren7 was established and verified by the analysis of cross-linked Cren7-DNA complexes by atomic force microscopy. Our results suggest that Cren7 differs significantly from Sul7, another chromatin protein conserved among Sulfolobus species, in both DNA binding and deformation. These data shed significant light on the strategy of chromosomal DNA organization in crenarchaea.
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Affiliation(s)
- Zhenfeng Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Mohan Zhao
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing, 100049, China
| | - Yuanyuan Chen
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Li Wang
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing, 100049, China
| | - Qinghua Liu
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing, 100049, China
| | - Yuhui Dong
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing, 100049, China
| | - Yong Gong
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing, 100049, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing, 100049, China
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20
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Rollie C, Graham S, Rouillon C, White MF. Prespacer processing and specific integration in a Type I-A CRISPR system. Nucleic Acids Res 2018; 46:1007-1020. [PMID: 29228332 PMCID: PMC5815122 DOI: 10.1093/nar/gkx1232] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/22/2017] [Accepted: 11/29/2017] [Indexed: 12/15/2022] Open
Abstract
The CRISPR-Cas system for prokaryotic adaptive immunity provides RNA-mediated protection from viruses and mobile genetic elements. Adaptation is dependent on the Cas1 and Cas2 proteins along with varying accessory proteins. Here we analyse the process in Sulfolobus solfataricus, showing that while Cas1 and Cas2 catalyze spacer integration in vitro, host factors are required for specificity. Specific integration also requires at least 400 bp of the leader sequence, and is dependent on the presence of hydrolysable ATP, suggestive of an active process that may involve DNA remodelling. Specific spacer integration is associated with processing of prespacer 3' ends in a PAM-dependent manner. This is reflected in PAM-dependent processing of prespacer 3' ends in vitro in the presence of cell lysate or the Cas4 nuclease, in a reaction consistent with PAM-directed binding and protection of prespacer DNA. These results highlight the diverse interplay between CRISPR-Cas elements and host proteins across CRISPR types.
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Affiliation(s)
- Clare Rollie
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Shirley Graham
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Christophe Rouillon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
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21
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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: 7] [Impact Index Per Article: 1.2] [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
![]()
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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22
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Han W, Xu Y, Feng X, Liang YX, Huang L, Shen Y, She Q. NQO-Induced DNA-Less Cell Formation Is Associated with Chromatin Protein Degradation and Dependent on A 0A 1-ATPase in Sulfolobus. Front Microbiol 2017; 8:1480. [PMID: 28855893 PMCID: PMC5557786 DOI: 10.3389/fmicb.2017.01480] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/24/2017] [Indexed: 12/29/2022] Open
Abstract
To investigate DNA damage response in the model crenarchaeon Sulfolobus islandicus, four different DNA damage agents were tested for their effects on cell death of this archaeon, including UV irradiation, methyl methanesulfonate, cisplatin, and 4-nitroquinoline 1-oxide (NQO). Cell death featured with DNA-less cell formation was revealed in DNA damage treatment with each agent. Cellular responses upon NQO treatment were characterized in details, and following sequential events were revealed, including: a modest accumulation of G1/S phase cells, membrane depolarization, proteolytic degradation of chromatin proteins, and chromosomal DNA degradation. Further insights into the process were gained from studying drugs that affect the archaeal ATP synthase, including a proton gradient uncoupler and an ATP synthase inhibitor. Whereas the proton uncoupler-mediated excess proton influx yielded cell death as observed for the NQO treatment, inhibition of ATP synthase attenuated NQO-induced membrane depolarization and DNA-less cell formation. In conclusion, the NQO-induced cell death in S. islandicus is characterized by proteolytic degradation of chromatin protein, and chromosomal DNA degradation, which probably represents a common feature for the cell death induced by different DNA damage agents.
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Affiliation(s)
- Wenyuan Han
- Archaea Centre, Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Yanqun Xu
- Archaea Centre, Department of Biology, University of CopenhagenCopenhagen, Denmark.,State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xu Feng
- Archaea Centre, Department of Biology, University of CopenhagenCopenhagen, Denmark.,State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Yun X Liang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Yulong Shen
- State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China
| | - Qunxin She
- Archaea Centre, Department of Biology, University of CopenhagenCopenhagen, Denmark.,State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
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23
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Roles of Leu28 side chain intercalation in the interaction between Cren7 and DNA. Biochem J 2017; 474:1727-1739. [PMID: 28377493 DOI: 10.1042/bcj20170036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/30/2017] [Accepted: 04/03/2017] [Indexed: 12/31/2022]
Abstract
Crenarchaeal chromatin protein Cren7 binds double-stranded DNA in the minor groove, introducing a sharp single-step DNA kink. The side chain of Leu28, a residue conserved among all Cren7 homologs, intercalates into the kinked DNA step. In the present study, we replaced Leu28 with a residue containing a hydrophobic side chain of different sizes (i.e. L28A, L28V, L28I, L28M and L28F). Both the stability of the Cren7-DNA complex and the ability of Cren7 to constrain DNA supercoils correlated well with the size of the intercalated side chain. Structural analysis shows that L28A induces a kink (∼43°), nearly as sharp as that produced by wild-type Cren7 (∼48°), in the bound DNA fragment despite the lack of side chain intercalation. In another duplex DNA fragment, L28F inserts a large hydrophobic side chain deep into the DNA step, but introduces a smaller kink (∼39°) than that formed by the wild-type protein (∼50°). Mutation of Leu28 into methionine yields two protein conformers differing in loop β3-β4 orientation, DNA-binding surface and DNA geometry in the protein-DNA structure. Our results indicate that side chain intercalation is not directly responsible for DNA kinking or bending by Cren7, but plays a critical role in the stabilization of the Cren7-DNA complex. In addition, the flexibility of loop β3-β4 in Cren7, as revealed in the crystal structure of L28M-DNA, may serve a role in the modulation of chromosomal organization and function in the cell.
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24
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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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25
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The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA. PLoS One 2017; 12:e0169627. [PMID: 28068385 PMCID: PMC5222340 DOI: 10.1371/journal.pone.0169627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 12/20/2016] [Indexed: 11/19/2022] Open
Abstract
The Sso7c4 from Sulfolobus solfataricus forms a dimer, which is believed to function as a chromosomal protein involved in genomic DNA compaction and gene regulation. Here, we present the crystal structure of wild-type Sso7c4 at a high resolution of 1.63 Å, showing that the two basic C-termini are disordered. Based on the fluorescence polarization (FP) binding assay, two arginine pairs, R11/R22' and R11'/R22, on the top surface participate in binding DNA. As shown in electron microscopy (EM) images, wild-type Sso7c4 compacts DNA through bridging and bending interactions, whereas the binding of C-terminally truncated proteins rigidifies and opens DNA molecules, and no compaction of the DNA occurs. Moreover, the FP, EM and fluorescence resonance energy transfer (FRET) data indicated that the two basic and flexible C-terminal arms of the Sso7c4 dimer play a crucial role in binding and bending DNA. Sso7c4 has been classified as a repressor-like protein because of its similarity to Escherichia coli Ecrep 6.8 and Ecrep 7.3 as well as Agrobacterium tumefaciens ACCR in amino acid sequence. Based on these data, we proposed a model of the Sso7c4-DNA complex using a curved DNA molecule in the catabolite activator protein-DNA complex. The DNA end-to-end distance measured with FRET upon wild-type Sso7c4 binding is almost equal to the distance measured in the model, which supports the fidelity of the proposed model. The FRET data also confirm the EM observation showing that the binding of wild-type Sso7c4 reduces the DNA length while the C-terminal truncation does not. A functional role for Sso7c4 in the organization of chromosomal DNA and/or the regulation of gene expression through bridging and bending interactions is suggested.
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26
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Tethered Particle Motion Analysis of the DNA Binding Properties of Architectural Proteins. Methods Mol Biol 2017; 1624:127-143. [PMID: 28842881 DOI: 10.1007/978-1-4939-7098-8_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Architectural DNA binding proteins are key to the organization and compaction of genomic DNA inside cells. Tethered Particle Motion (TPM) permits analysis of DNA conformation and detection of changes in conformation induced by such proteins at the single molecule level in vitro. As many individual protein-DNA complexes can be investigated in parallel, these experiments have high throughput. TPM is therefore well suited for characterization of the effects of protein-DNA stoichiometry and changes in physicochemical conditions (pH, osmolarity, and temperature). Here, we describe in detail how to perform Tethered Particle Motion experiments on complexes between DNA and architectural proteins to determine their structural and biochemical characteristics.
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27
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Turaga G, Edmondson SP, Smith K, Shriver JW. Insights into the Structure of Sulfolobus Nucleoid Using Engineered Sac7d Dimers with a Defined Orientation. Biochemistry 2016; 55:6230-6237. [PMID: 27766846 DOI: 10.1021/acs.biochem.6b00810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The structure of Archaeal chromatin or nucleoid is believed to have characteristics similar to that found in both eukaryotes and bacteria. Recent comparative studies have suggested that DNA compaction in Archaea requires a bridging protein (e.g., Alba) along with either a wrapping protein (e.g., a histone) or a bending protein such as Sac7d. While X-ray crystal structures demonstrate that Sac7d binds as a monomer to create a significant kink in duplex DNA, the structure of a multiprotein-DNA complex has not been established. Using cross-linked dimers of Sac7d with a defined orientation, we present evidence that indicates that Sac7d is able to largely coat duplex DNA in vivo by binding in alternating head-to-head and tail-to-tail orientations. Although each Sac7d monomer promotes a significant kink of nearly 70°, coated DNA is expected to be largely extended because of compensation of repetitive kinks with helical symmetry.
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Affiliation(s)
- Gokul Turaga
- Departments of Chemistry and Biological Sciences, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
| | - Stephen P Edmondson
- Departments of Chemistry and Biological Sciences, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
| | - Kelley Smith
- Departments of Chemistry and Biological Sciences, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
| | - John W Shriver
- Departments of Chemistry and Biological Sciences, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
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Driessen RPC, Lin SN, Waterreus WJ, van der Meulen ALH, van der Valk RA, Laurens N, Moolenaar GF, Pannu NS, Wuite GJL, Goosen N, Dame RT. Diverse architectural properties of Sso10a proteins: Evidence for a role in chromatin compaction and organization. Sci Rep 2016; 6:29422. [PMID: 27403582 PMCID: PMC4941522 DOI: 10.1038/srep29422] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/17/2016] [Indexed: 11/19/2022] Open
Abstract
Sso10a proteins are small DNA-binding proteins expressed by the crenarchaeal model organism Sulfolobus solfataricus. Based on the structure of Sso10a1, which contains a winged helix-turn-helix motif, it is believed that Sso10a proteins function as sequence-specific transcription factors. Here we show that Sso10a1 and Sso10a2 exhibit different distinct DNA-binding modes. While the ability to bend DNA is shared between the two proteins, DNA bridging is observed only for Sso10a1 and only Sso10a2 exhibits filament formation along DNA. The architectural properties of Sso10a proteins suggest that these proteins fulfil generic roles in chromatin organization and compaction. As these proteins exhibit different binding behaviour depending on their DNA binding stoichiometry, altered levels of expression in the cell can be exploited to drive changes in local genome folding, which may operate to modulate transcription.
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Affiliation(s)
- Rosalie P C Driessen
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Szu-Ning Lin
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.,Department of Physics and Astronomy, VU University, Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Willem-Jan Waterreus
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alson L H van der Meulen
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Ramon A van der Valk
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Niels Laurens
- Department of Physics and Astronomy, VU University, Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Geri F Moolenaar
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Navraj S Pannu
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, VU University, Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Nora Goosen
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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SURESH GORLE, PRIYAKUMAR UDEVA. Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme. J CHEM SCI 2015. [DOI: 10.1007/s12039-015-0942-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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30
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van der Valk RA, Vreede J, Crémazy F, Dame RT. Genomic Looping: A Key Principle of Chromatin Organization. J Mol Microbiol Biotechnol 2015; 24:344-59. [DOI: 10.1159/000368851] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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31
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Insights into the interaction between Cren7 and DNA: the role of loop β3-β4. Extremophiles 2015; 19:395-406. [PMID: 25555709 DOI: 10.1007/s00792-014-0725-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
Abstract
Sulfolobus synthesizes large amounts of small chromatin proteins Cren7 and Sul7d. The two proteins share overall structural similarity, but differ distinctly in the DNA-binding region between β3- and β4-strands. While Sul7d possesses a hinge of two amino acid residues, Cren7 contains a flexible seven-residue loop (loop β3-β4) in the region. Here, we report the role of loop β3-β4 in the interaction of Cren7 with duplex DNA. We show that all residues with a large side chain on the loop, i.e., Pro30, Lys31, Arg33 and Lys34, contributed significantly to the binding of Cren7 to DNA. The three basic amino acids affected the ability of Cren7 to constrain negative DNA supercoils in a residue number-dependent manner. The crystal structure of a complex between a mutant Cren7 protein (GR) with loop β3-β4 replaced by two residues (Gly and Arg) to mimic the hinge at the corresponding position in Sul7d and an 8-bp dsDNA has been determined. Structural comparison between the GR-DNA and Cren7-DNA complexes shows that GR resembles Sul7d more than Cren7 in DNA-binding size and in the effect on the width of the major groove of DNA and the pattern of DNA bending. However, GR induces smaller DNA curvature than Sul7d. Our results suggest that Cren7 and Sul7d package chromosomal DNA in a slightly different fashion, presumably permitting different chromosomal accessibility by proteins functioning in DNA transactions.
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Driessen RPC, Sitters G, Laurens N, Moolenaar GF, Wuite GJL, Goosen N, Dame RT. Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins. Biochemistry 2014; 53:6430-8. [PMID: 25291500 PMCID: PMC5451147 DOI: 10.1021/bi500344j] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
The
helical structure of double-stranded DNA is destabilized by
increasing temperature. Above a critical temperature (the melting
temperature), the two strands in duplex DNA become fully separated.
Below this temperature, the structural effects are localized. Using
tethered particle motion in a temperature-controlled sample chamber,
we systematically investigated the effect of increasing temperature
on DNA structure and the interplay between this effect and protein
binding. Our measurements revealed that (1) increasing temperature
enhances DNA flexibility, effectively leading to more compact folding
of the double-stranded DNA chain, and (2) temperature differentially
affects different types of DNA-bending chromatin proteins from mesophilic
and thermophilic organisms. Thus, our findings aid in understanding
genome organization in organisms thriving at moderate as well as extreme
temperatures. Moreover, our results underscore the importance of carefully
controlling and measuring temperature in single-molecule DNA (micromanipulation)
experiments.
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Affiliation(s)
- Rosalie P C Driessen
- Molecular Genetics, Leiden Institute of Chemistry and Cell Observatory, Leiden University , 2333 CC Leiden, The Netherlands
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Chromatin structure and dynamics in hot environments: architectural proteins and DNA topoisomerases of thermophilic archaea. Int J Mol Sci 2014; 15:17162-87. [PMID: 25257534 PMCID: PMC4200833 DOI: 10.3390/ijms150917162] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/19/2014] [Accepted: 09/09/2014] [Indexed: 01/20/2023] Open
Abstract
In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.
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34
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Mechanosensing of DNA bending in a single specific protein-DNA complex. Sci Rep 2013; 3:3508. [PMID: 24336435 PMCID: PMC3863814 DOI: 10.1038/srep03508] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 11/29/2013] [Indexed: 01/10/2023] Open
Abstract
Many crucial biological processes are regulated by mechanical stimuli. Here, we report new findings that pico-Newton forces can drastically affect the stability of the site-specific DNA binding of a single transcription factor, the E. coli integration host factor (IHF), by stretching a short ~150 nm DNA containing a single IHF binding site. Dynamic binding and unbinding of single IHF were recorded and analyzed for the force-dependent stability of the IHF-DNA complex. Our results demonstrate that the IHF-DNA interaction is fine tuned by force in different salt concentration and temperature over physiological ranges, indicating that, besides other physiological factors, force may play equally important role in transcription regulation. These findings have broad implications with regard to general mechanosensitivity of site-specific DNA bending proteins.
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Abstract
Crenarchaeal genomes are organized into a compact nucleoid by a set of small chromatin proteins. Although there is little knowledge of chromatin structure in Archaea, similarities between crenarchaeal and bacterial chromatin proteins suggest that organization and regulation could be achieved by similar mechanisms. In the present review, we describe the molecular properties of crenarchaeal chromatin proteins and discuss the possible role of these architectural proteins in organizing the crenarchaeal chromatin and in gene regulation.
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Sun F, Huang L. Sulfolobus chromatin proteins modulate strand displacement by DNA polymerase B1. Nucleic Acids Res 2013; 41:8182-95. [PMID: 23821667 PMCID: PMC3783171 DOI: 10.1093/nar/gkt588] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Strand displacement by a DNA polymerase serves a key role in Okazaki fragment maturation, which involves displacement of the RNA primer of the preexisting Okazaki fragment into a flap structure, and subsequent flap removal and fragment ligation. We investigated the role of Sulfolobus chromatin proteins Sso7d and Cren7 in strand displacement by DNA polymerase B1 (PolB1) from the hyperthermophilic archaeon Sulfolobus solfataricus. PolB1 showed a robust strand displacement activity and was capable of synthesizing thousands of nucleotides on a DNA-primed 72-nt single-stranded circular DNA template. This activity was inhibited by both Sso7d and Cren7, which limited the flap length to 3–4 nt at saturating concentrations. However, neither protein inhibited RNA displacement on an RNA-primed single-stranded DNA minicircle by PolB1. Strand displacement remained sensitive to modulation by the chromatin proteins when PolB1 was in association with proliferating cell nuclear antigen. Inhibition of DNA instead of RNA strand displacement by the chromatin proteins is consistent with the finding that double-stranded DNA was more efficiently bound and stabilized than an RNA:DNA duplex by these proteins. Our results suggest that Sulfolobus chromatin proteins modulate strand displacement by PolB1, permitting efficient removal of the RNA primer while inhibiting excessive displacement of the newly synthesized DNA strand during Okazaki fragment maturation.
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Affiliation(s)
- Fei Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Niu Y, Xia Y, Wang S, Li J, Niu C, Li X, Zhao Y, Xiong H, Li Z, Lou H, Cao Q. A prototypic lysine methyltransferase 4 from archaea with degenerate sequence specificity methylates chromatin proteins Sul7d and Cren7 in different patterns. J Biol Chem 2013; 288:13728-40. [PMID: 23530048 DOI: 10.1074/jbc.m113.452979] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The origin of eukaryotic histone modification enzymes still remains obscure. RESULTS Prototypic KMT4/Dot1 from Archaea targets chromatin proteins (Sul7d and Cren7) and shows increased activity on Sul7d, but not Cren7, in the presence of DNA. CONCLUSION Promiscuous aKMT4 could be regulated by chromatin environment. SIGNIFICANCE This study supports the prokaryotic origin model of eukaryotic histone methyltransferases and sheds light on chromatin dynamics in Archaea. Histone methylation is one of the major epigenetic modifications even in early diverging unicellular eukaryotes. We show that a widespread lysine methyltransferase from Archaea (aKMT4), bears striking structural and functional resemblance to the core of distantly related eukaryotic KMT4/Dot1. aKMT4 methylates a set of various proteins, including the chromatin proteins Sul7d and Cren7, and RNA exosome components. Csl4- and Rrp4-exosome complexes are methylated in different patterns. aKMT4 can self-methylate intramolecularly and compete with other proteins for the methyl group. Automethylation is inhibited by suitable substrates or DNA in a concentration-dependent manner. The automethylated enzyme shows relatively compromised activity. aKMT4-8A mutant with abrogated automethylation shows a more than 150% increase in methylation of substrates, suggesting a possible mechanism to regulate methyltransferase activity. More interestingly, methylation of Sul7d, but not Cren7, by aKMT4 is significantly enhanced by DNA. MS/MS and kinetic analysis further suggest that aKMT4 methylates Sul7d in the chromatin context. These data provide a clue to the possible regulation of aKMT4 activity by the local chromatin environment, albeit as a promiscuous enzyme required for extensive and variegated lysine methylation in Sulfolobus. This study supports the prokaryotic origin model of eukaryotic histone modification enzymes and sheds light on regulation of archaeal chromatin.
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Affiliation(s)
- Yanling Niu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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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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