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Schwab S, Hu Y, van Erp B, Cajili MKM, Hartmann MD, Hernandez Alvarez B, Alva V, Boyle AL, Dame RT. Histones and histone variant families in prokaryotes. Nat Commun 2024; 15:7950. [PMID: 39261503 PMCID: PMC11390915 DOI: 10.1038/s41467-024-52337-y] [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: 07/10/2023] [Accepted: 08/30/2024] [Indexed: 09/13/2024] Open
Abstract
Histones are important chromatin-organizing proteins in eukaryotes and archaea. They form superhelical structures around which DNA is wrapped. Recent studies have shown that some archaea and bacteria contain alternative histones that exhibit different DNA binding properties, in addition to highly divergent sequences. However, the vast majority of these histones are identified in metagenomes and thus are difficult to study in vivo. The recent revolutionary breakthroughs in computational protein structure prediction by AlphaFold2 and RoseTTAfold allow for unprecedented insights into the potential function and structure of previously uncharacterized proteins. Here, we categorize the prokaryotic histone space into 17 distinct groups based on AlphaFold2 predictions. We identify a superfamily of histones, termed α3 histones, which are common in archaea and present in several bacteria. Importantly, we establish the existence of a large family of histones throughout archaea and in some bacteriophages that, instead of wrapping DNA, bridge DNA, thereby diverging from conventional nucleosomal histones.
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Affiliation(s)
- Samuel Schwab
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Yimin Hu
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Bert van Erp
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Marc K M Cajili
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, 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
| | - 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
| | - Aimee L Boyle
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
- School of Chemistry, University of Bristol, Bristol, UK
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, 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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2
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Ghilain C, Vidal-Cruchez O, Joly A, Debatisse M, Gilson E, Giraud-Panis MJ. Innovative Tools for DNA Topology Probing in Human Cells Reveal a Build-Up of Positive Supercoils Following Replication Stress at Telomeres and at the FRA3B Fragile Site. Cells 2024; 13:1361. [PMID: 39195250 DOI: 10.3390/cells13161361] [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: 07/24/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024] Open
Abstract
Linear unconstrained DNA cannot harbor supercoils since these supercoils can diffuse and be eliminated by free rotation of the DNA strands at the end of the molecule. Mammalian telomeres, despite constituting the ends of linear chromosomes, can hold supercoils and be subjected to topological stress. While negative supercoiling was previously observed, thus proving the existence of telomeric topological constraints, positive supercoils were never probed due to the lack of an appropriate tool. Indeed, the few tools available currently could only investigate unwound (Trioxsalen) or overwound (GapR) DNA topology (variations in twist) but not the variations in writhe (supercoils and plectonemes). To address this question, we have designed innovative tools aimed at analyzing both positive and negative DNA writhe in cells. Using them, we could observe the build-up of positive supercoils following replication stress and inhibition of Topoisomerase 2 on telomeres. TRF2 depletion caused both telomere relaxation and an increase in positive supercoils while the inhibition of Histone Deacetylase I and II by TSA only caused telomere relaxation. Moving outside telomeres, we also observed a build-up of positive supercoils on the FRA3B fragile site following replication stress, suggesting a topological model of DNA fragility for this site.
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Affiliation(s)
- Claire Ghilain
- CNRS UMR7284/INSERM U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Faculty of Medicine, University Côte d'Azur, 06107 Nice, France
| | | | - Aurélia Joly
- Medical Microbiology and Immunology Department, Faculty of Medicine & Dentistry, University of Alberta, 116 St. and 85 Ave., Edmonton, AB T6G 2R3, Canada
| | - Michelle Debatisse
- Gustave Roussy Institute, Sorbonne Université, UPMC, 94805 Villejuif, France
| | - Eric Gilson
- CNRS UMR7284/INSERM U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Faculty of Medicine, University Côte d'Azur, 06107 Nice, France
- Department of Geriatrics, Medical Center on Aging of Shanghai Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200025, China
- International Research Project in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, Ruijin Hospital, Shanghai Jiao Tong University School, Shanghai 200025, China
- Department of Genetics, CHU, FHU OncoAge, 06000 Nice, France
| | - Marie-Josèphe Giraud-Panis
- CNRS UMR7284/INSERM U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Faculty of Medicine, University Côte d'Azur, 06107 Nice, France
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3
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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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4
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Schwab S, Dame RT. Identification, characterization and classification of prokaryotic nucleoid-associated proteins. Mol Microbiol 2024. [PMID: 39039769 DOI: 10.1111/mmi.15298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/02/2024] [Accepted: 07/06/2024] [Indexed: 07/24/2024]
Abstract
Common throughout life is the need to compact and organize the genome. Possible mechanisms involved in this process include supercoiling, phase separation, charge neutralization, macromolecular crowding, and nucleoid-associated proteins (NAPs). NAPs are special in that they can organize the genome at multiple length scales, and thus are often considered as the architects of the genome. NAPs shape the genome by either bending DNA, wrapping DNA, bridging DNA, or forming nucleoprotein filaments on the DNA. In this mini-review, we discuss recent advancements of unique NAPs with differing architectural properties across the tree of life, including NAPs from bacteria, archaea, and viruses. To help the characterization of NAPs from the ever-increasing number of metagenomes, we recommend a set of cheap and simple in vitro biochemical assays that give unambiguous insights into the architectural properties of NAPs. Finally, we highlight and showcase the usefulness of AlphaFold in the characterization of novel NAPs.
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Affiliation(s)
- Samuel Schwab
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, 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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5
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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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6
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Henneman B, Erkelens AM, Heinsman J, Battjes J, Dame RT. Quantitation of DNA Binding Affinity Using Tethered Particle Motion. Methods Mol Biol 2024; 2819:497-518. [PMID: 39028521 DOI: 10.1007/978-1-0716-3930-6_23] [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
The binding constant is an important characteristic of a DNA-binding protein. A large number of methods exist to measure the binding constant, but many of those methods have intrinsic flaws that influence the outcome of the characterization. Tethered particle motion (TPM) is a simple, cheap, and high-throughput single-molecule method that can be used to measure binding constants of proteins binding to DNA reliably, provided that they distort DNA. In TPM, the motion of a bead tethered to a surface by DNA is tracked using light microscopy. A protein binding to the DNA will alter bead motion. This change in bead motion makes it possible to measure the DNA-binding properties of proteins. We use the bacterial protein integration host factor (IHF) and the archaeal histone HMfA as examples to show how specific binding to DNA can be measured. Moreover, we show how the end-to-end distance can provide structural insights into protein-DNA binding.
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Affiliation(s)
- Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Amanda M Erkelens
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Joost Heinsman
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Julius Battjes
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, 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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Baum B, Spang A. On the origin of the nucleus: a hypothesis. Microbiol Mol Biol Rev 2023; 87:e0018621. [PMID: 38018971 PMCID: PMC10732040 DOI: 10.1128/mmbr.00186-21] [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] [Indexed: 11/30/2023] Open
Abstract
SUMMARYIn this hypothesis article, we explore the origin of the eukaryotic nucleus. In doing so, we first look afresh at the nature of this defining feature of the eukaryotic cell and its core functions-emphasizing the utility of seeing the eukaryotic nucleoplasm and cytoplasm as distinct regions of a common compartment. We then discuss recent progress in understanding the evolution of the eukaryotic cell from archaeal and bacterial ancestors, focusing on phylogenetic and experimental data which have revealed that many eukaryotic machines with nuclear activities have archaeal counterparts. In addition, we review the literature describing the cell biology of representatives of the TACK and Asgardarchaeaota - the closest known living archaeal relatives of eukaryotes. Finally, bringing these strands together, we propose a model for the archaeal origin of the nucleus that explains much of the current data, including predictions that can be used to put the model to the test.
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Affiliation(s)
- Buzz Baum
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
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8
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Watts EA, Garrett SC, Catchpole RJ, Clark LM, Sanders TJ, Marshall CJ, Wenck BR, Vickerman RL, Santangelo TJ, Fuchs R, Robb B, Olson S, Graveley BR, Terns MP. Histones direct site-specific CRISPR spacer acquisition in model archaeon. Nat Microbiol 2023; 8:1682-1694. [PMID: 37550505 PMCID: PMC10823912 DOI: 10.1038/s41564-023-01446-3] [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: 10/27/2022] [Accepted: 07/11/2023] [Indexed: 08/09/2023]
Abstract
CRISPR-Cas systems provide heritable immunity against viruses and other mobile genetic elements by incorporating fragments of invader DNA into the host CRISPR array as spacers. Integration of new spacers is localized to the 5' end of the array, and in certain Gram-negative Bacteria this polarized localization is accomplished by the integration host factor. For most other Bacteria and Archaea, the mechanism for 5' end localization is unknown. Here we show that archaeal histones play a key role in directing integration of CRISPR spacers. In Pyrococcus furiosus, deletion of either histone A or B impairs integration. In vitro, purified histones are sufficient to direct integration to the 5' end of the CRISPR array. Archaeal histone tetramers and bacterial integration host factor induce similar U-turn bends in bound DNA. These findings indicate a co-evolution of CRISPR arrays with chromosomal DNA binding proteins and a widespread role for binding and bending of DNA to facilitate accurate spacer integration.
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The Hypersaline Archaeal Histones HpyA and HstA Are DNA Binding Proteins That Defy Categorization According to Commonly Used Functional Criteria. mBio 2023; 14:e0344922. [PMID: 36779711 PMCID: PMC10128011 DOI: 10.1128/mbio.03449-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
Histone proteins are found across diverse lineages of Archaea, many of which package DNA and form chromatin. However, previous research has led to the hypothesis that the histone-like proteins of high-salt-adapted archaea, or halophiles, function differently. The sole histone protein encoded by the model halophilic species Halobacterium salinarum, HpyA, is nonessential and expressed at levels too low to enable genome-wide DNA packaging. Instead, HpyA mediates the transcriptional response to salt stress. Here we compare the features of genome-wide binding of HpyA to those of HstA, the sole histone of another model halophile, Haloferax volcanii. hstA, like hpyA, is a nonessential gene. To better understand HpyA and HstA functions, protein-DNA binding data (chromatin immunoprecipitation sequencing [ChIP-seq]) of these halophilic histones are compared to publicly available ChIP-seq data from DNA binding proteins across all domains of life, including transcription factors (TFs), nucleoid-associated proteins (NAPs), and histones. These analyses demonstrate that HpyA and HstA bind the genome infrequently in discrete regions, which is similar to TFs but unlike NAPs, which bind a much larger genomic fraction. However, unlike TFs that typically bind in intergenic regions, HpyA and HstA binding sites are located in both coding and intergenic regions. The genome-wide dinucleotide periodicity known to facilitate histone binding was undetectable in the genomes of both species. Instead, TF-like and histone-like binding sequence preferences were detected for HstA and HpyA, respectively. Taken together, these data suggest that halophilic archaeal histones are unlikely to facilitate genome-wide chromatin formation and that their function defies categorization as a TF, NAP, or histone. IMPORTANCE Most cells in eukaryotic species-from yeast to humans-possess histone proteins that pack and unpack DNA in response to environmental cues. These essential proteins regulate genes necessary for important cellular processes, including development and stress protection. Although the histone fold domain originated in the domain of life Archaea, the function of archaeal histone-like proteins is not well understood relative to those of eukaryotes. We recently discovered that, unlike histones of eukaryotes, histones in hypersaline-adapted archaeal species do not package DNA and can act as transcription factors (TFs) to regulate stress response gene expression. However, the function of histones across species of hypersaline-adapted archaea still remains unclear. Here, we compare hypersaline histone function to a variety of DNA binding proteins across the tree of life, revealing histone-like behavior in some respects and specific transcriptional regulatory function in others.
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Armeev GA, Gribkova AK, Shaytan AK. Nucleosomes and their complexes in the cryoEM era: Trends and limitations. Front Mol Biosci 2022; 9:1070489. [PMID: 36504712 PMCID: PMC9730872 DOI: 10.3389/fmolb.2022.1070489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/09/2022] [Indexed: 11/25/2022] Open
Abstract
Twenty-five years have passed since the appearance of the first atomistic model of the nucleosome structure, and since then the number of new structures has gradually increased. With the advent of cryo-microscopy, the rate of accumulation of models has increased significantly. New structures are emerging with different histone variants and a variety of proteins that bind to nucleosomes. At the moment, there are more than four hundred structures containing nucleosomes in the Protein Data Bank. Many of these structures represent similar complexes, others differ in composition, conformation and quality. In this perspective, we investigate the diversity of known nucleosome structures, analyze data and model quality, variations in histone/DNA content of nucleosomes and spectrum of their interactors. We outline those parts of the nucleosome "structurome" that are already explored and those awaiting further exploration.
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Affiliation(s)
- Grigoriy A. Armeev
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,*Correspondence: Grigoriy A. Armeev, ; Alexey K. Shaytan,
| | - Anna K. Gribkova
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey K. Shaytan
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Computer Science, HSE University, Moscow, Russia,*Correspondence: Grigoriy A. Armeev, ; Alexey K. Shaytan,
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11
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Hocher A, Borrel G, Fadhlaoui K, Brugère JF, Gribaldo S, Warnecke T. Growth temperature and chromatinization in archaea. Nat Microbiol 2022; 7:1932-1942. [PMID: 36266339 PMCID: PMC7613761 DOI: 10.1038/s41564-022-01245-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/07/2022] [Indexed: 11/08/2022]
Abstract
DNA in cells is associated with proteins that constrain its structure and affect DNA-templated processes including transcription and replication. HU and histones are the main constituents of chromatin in bacteria and eukaryotes, respectively, with few exceptions. Archaea, in contrast, have diverse repertoires of nucleoid-associated proteins (NAPs). To analyse the evolutionary and ecological drivers of this diversity, we combined a phylogenomic survey of known and predicted NAPs with quantitative proteomic data. We identify the Diaforarchaea as a hotbed of NAP gain and loss, and experimentally validate candidate NAPs in two members of this clade, Thermoplasma volcanium and Methanomassiliicoccus luminyensis. Proteomic analysis across a diverse sample of 19 archaea revealed that NAP investment varies from <0.03% to >5% of total protein. This variation is predicted by growth temperature. We propose that high levels of chromatinization have evolved as a mechanism to prevent uncontrolled helix denaturation at higher temperatures, with implications for the origin of chromatin in both archaea and eukaryotes.
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Affiliation(s)
- Antoine Hocher
- Medical Research Council London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, UMR CNRS6047, Evolutionary Biology of the Microbial Cell, Paris, France
| | - Khaled Fadhlaoui
- Université Clermont Auvergne, CNRS, Lab Microorganismes: Génome et Environnement LMGE, Clermont-Ferrand, France
| | - Jean-François Brugère
- Université Clermont Auvergne, CNRS, Lab Microorganismes: Génome et Environnement LMGE, Clermont-Ferrand, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, UMR CNRS6047, Evolutionary Biology of the Microbial Cell, Paris, France
| | - Tobias Warnecke
- Medical Research Council London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
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Sato S, Dacher M, Kurumizaka H. Nucleosome Structures Built from Highly Divergent Histones: Parasites and Giant DNA Viruses. EPIGENOMES 2022; 6:22. [PMID: 35997368 PMCID: PMC9396995 DOI: 10.3390/epigenomes6030022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 02/04/2023] Open
Abstract
In eukaryotes, genomic DNA is bound with histone proteins and packaged into chromatin. The nucleosome, a fundamental unit of chromatin, regulates the accessibility of DNA to enzymes involved in gene regulation. During the past few years, structural analyses of chromatin architectures have been limited to evolutionarily related organisms. The amino acid sequences of histone proteins are highly conserved from humans to yeasts, but are divergent in the deeply branching protozoan groups, including human parasites that are directly related to human health. Certain large DNA viruses, as well as archaeal organisms, contain distant homologs of eukaryotic histone proteins. The divergent sequences give rise to unique and distinct nucleosome architectures, although the fundamental principles of histone folding and DNA contact are highly conserved. In this article, we review the structures and biophysical properties of nucleosomes containing histones from the human parasites Giardia lamblia and Leishmania major, and histone-like proteins from the Marseilleviridae amoeba virus family. The presented data confirm the sharing of the overall DNA compaction system among evolutionally distant species and clarify the deviations from the species-specific nature of the nucleosome.
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Affiliation(s)
| | | | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; (S.S.); (M.D.)
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13
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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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14
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Sakrikar S, Schmid A. An archaeal histone-like protein regulates gene expression in response to salt stress. Nucleic Acids Res 2021; 49:12732-12743. [PMID: 34883507 PMCID: PMC8682779 DOI: 10.1093/nar/gkab1175] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 12/21/2022] Open
Abstract
Histones, ubiquitous in eukaryotes as DNA-packing proteins, find their evolutionary origins in archaea. Unlike the characterized histone proteins of a number of methanogenic and themophilic archaea, previous research indicated that HpyA, the sole histone encoded in the model halophile Halobacterium salinarum, is not involved in DNA packaging. Instead, it was found to have widespread but subtle effects on gene expression and to maintain wild type cell morphology. However, the precise function of halophilic histone-like proteins remain unclear. Here we use quantitative phenotyping, genetics, and functional genomics to investigate HpyA function. These experiments revealed that HpyA is important for growth and rod-shaped morphology in reduced salinity. HpyA preferentially binds DNA at discrete genomic sites under low salt to regulate expression of ion uptake, particularly iron. HpyA also globally but indirectly activates other ion uptake and nucleotide biosynthesis pathways in a salt-dependent manner. Taken together, these results demonstrate an alternative function for an archaeal histone-like protein as a transcriptional regulator, with its function tuned to the physiological stressors of the hypersaline environment.
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Affiliation(s)
- Saaz Sakrikar
- Biology Department, Duke University, Durham, NC27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC27708, USA
| | - Amy K Schmid
- Biology Department, Duke University, Durham, NC27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC27708, USA
- Center for Genomics and Computational Biology, Duke University, Durham, NC27708, USA
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15
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Maruyama H, Nambu T, Mashimo C, Okinaga T, Takeyasu K. Single-Molecule/Cell Analyses Reveal Principles of Genome-Folding Mechanisms in the Three Domains of Life. Int J Mol Sci 2021; 22:13432. [PMID: 34948225 PMCID: PMC8707338 DOI: 10.3390/ijms222413432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 11/21/2022] Open
Abstract
Comparative structural/molecular biology by single-molecule analyses combined with single-cell dissection, mass spectroscopy, and biochemical reconstitution have been powerful tools for elucidating the mechanisms underlying genome DNA folding. All genomes in the three domains of life undergo stepwise folding from DNA to 30-40 nm fibers. Major protein players are histone (Eukarya and Archaea), Alba (Archaea), and HU (Bacteria) for fundamental structural units of the genome. In Euryarchaeota, a major archaeal phylum, either histone or HTa (the bacterial HU homolog) were found to wrap DNA. This finding divides archaea into two groups: those that use DNA-wrapping as the fundamental step in genome folding and those that do not. Archaeal transcription factor-like protein TrmBL2 has been suggested to be involved in genome folding and repression of horizontally acquired genes, similar to bacterial H-NS protein. Evolutionarily divergent SMC proteins contribute to the establishment of higher-order structures. Recent results are presented, including the use of Hi-C technology to reveal that archaeal SMC proteins are involved in higher-order genome folding, and the use of single-molecule tracking to reveal the detailed functions of bacterial and eukaryotic SMC proteins. Here, we highlight the similarities and differences in the DNA-folding mechanisms in the three domains of life.
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Affiliation(s)
- Hugo Maruyama
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Takayuki Nambu
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Chiho Mashimo
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Toshinori Okinaga
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Kunio Takeyasu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan;
- Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan
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16
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Stevens KM, Hocher A, Warnecke T. Deep conservation of histone variants in Thermococcales archaea. Genome Biol Evol 2021; 14:6459647. [PMID: 34894218 PMCID: PMC8775648 DOI: 10.1093/gbe/evab274] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 11/12/2022] Open
Abstract
Histones are ubiquitous in eukaryotes where they assemble into nucleosomes, binding and wrapping DNA to form chromatin. One process to modify chromatin and regulate DNA accessibility is the replacement of histones in the nucleosome with paralogous variants. Histones are also present in archaea but whether and how histone variants contribute to the generation of different physiologically relevant chromatin states in these organisms remains largely unknown. Conservation of paralogs with distinct properties can provide prima facie evidence for defined functional roles. We recently revealed deep conservation of histone paralogs with different properties in the Methanobacteriales, but little is known experimentally about these histones. In contrast, the two histones of the model archaeon Thermococcus kodakarensis, HTkA and HTkB, have been examined in some depth, both in vitro and in vivo. HTkA and HTkB exhibit distinct DNA-binding behaviors and elicit unique transcriptional responses when deleted. Here, we consider the evolution of HTkA/B and their orthologs across the order Thermococcales. We find histones with signature HTkA- and HTkB-like properties to be present in almost all Thermococcales genomes. Phylogenetic analysis indicates the presence of one HTkA- and one HTkB-like histone in the ancestor of Thermococcales and long-term maintenance of these two paralogs throughout Thermococcales diversification. Our results support the notion that archaea and eukaryotes have convergently evolved histone variants that carry out distinct adaptive functions. Intriguingly, we also detect more highly diverged histone-fold proteins, related to those found in some bacteria, in several Thermococcales genomes. The functions of these bacteria-type histones remain unknown, but structural modeling suggests that they can form heterodimers with HTkA/B-like histones.
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Affiliation(s)
- Kathryn M Stevens
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Antoine Hocher
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Tobias Warnecke
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
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17
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Mao AW, Barck H, Young J, Paley A, Mao JH, Chang H. Identification of a novel cancer microbiome signature for predicting prognosis of human breast cancer patients. Clin Transl Oncol 2021; 24:597-604. [PMID: 34741726 DOI: 10.1007/s12094-021-02725-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/16/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Prognosis of breast cancer (BC) patients differs considerably and identifying reliable prognostic biomarker(s) is imperative. With evidence that the microbiome plays a critical role in the response to cancer therapies, we aimed to identify a cancer microbiome signature for predicting the prognosis of BC patients. METHODS The TCGA BC microbiome data (TCGA-BRCA-microbiome) was downloaded from cBioPortal. Univariate and multivariate Cox regression analyses were used to examine association of microbial abundance with overall survival (OS) and to identify a microbial signature for creating a prognostic scoring model. The performance of the scoring model was assessed by the area under the ROC curve (AUC). Nomograms using the microbial signature, clinical factors, and molecular subtypes were established to predict OS and progression-free survival (PFS). RESULTS Among 1406 genera, the abundances of 94 genera were significantly associated with BC patient OS in TCGA-BRCA-microbiome dataset. From that set we identified a 15-microbe prognostic signature and developed a 15-microbial abundance prognostic scoring (MAPS) model. Patients in low-risk group significantly prolong OS and PFS as compared to those in high-risk group. The time-dependent ROC curves with MAPS showed good predictive efficacy both in OS and PFS. Moreover, MAPS is an independent prognostic factor for OS and PFS over clinical factors and PAM50-based molecular subtypes and superior to the previously published 12-gene signature. The integration of MAPS into nomograms significantly improved prognosis prediction. CONCLUSION MAPS was successfully established to have independent prognostic value, and our study provides a new avenue for developing prognostic biomarkers by microbiome profiling.
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Affiliation(s)
- A W Mao
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - H Barck
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J Young
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - A Paley
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J -H Mao
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - H Chang
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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18
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Duprey A, Groisman EA. The regulation of DNA supercoiling across evolution. Protein Sci 2021; 30:2042-2056. [PMID: 34398513 PMCID: PMC8442966 DOI: 10.1002/pro.4171] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 11/11/2022]
Abstract
DNA supercoiling controls a variety of cellular processes, including transcription, recombination, chromosome replication, and segregation, across all domains of life. As a physical property, DNA supercoiling alters the double helix structure by under- or over-winding it. Intriguingly, the evolution of DNA supercoiling reveals both similarities and differences in its properties and regulation across the three domains of life. Whereas all organisms exhibit local, constrained DNA supercoiling, only bacteria and archaea exhibit unconstrained global supercoiling. DNA supercoiling emerges naturally from certain cellular processes and can also be changed by enzymes called topoisomerases. While structurally and mechanistically distinct, topoisomerases that dissipate excessive supercoils exist in all domains of life. By contrast, topoisomerases that introduce positive or negative supercoils exist only in bacteria and archaea. The abundance of topoisomerases is also transcriptionally and post-transcriptionally regulated in domain-specific ways. Nucleoid-associated proteins, metabolites, and physicochemical factors influence DNA supercoiling by acting on the DNA itself or by impacting the activity of topoisomerases. Overall, the unique strategies that organisms have evolved to regulate DNA supercoiling hold significant therapeutic potential, such as bactericidal agents that target bacteria-specific processes or anticancer drugs that hinder abnormal DNA replication by acting on eukaryotic topoisomerases specialized in this process. The investigation of DNA supercoiling therefore reveals general principles, conserved mechanisms, and kingdom-specific variations relevant to a wide range of biological questions.
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Affiliation(s)
- Alexandre Duprey
- Department of Microbial PathogenesisYale School of MedicineNew HavenConnecticutUSA
| | - Eduardo A. Groisman
- Department of Microbial PathogenesisYale School of MedicineNew HavenConnecticutUSA
- Yale Microbial Sciences InstituteWest HavenConnecticutUSA
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19
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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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20
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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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21
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Loth K, Largillière J, Coste F, Culard F, Landon C, Castaing B, Delmas AF, Paquet F. New protein-DNA complexes in archaea: a small monomeric protein induces a sharp V-turn DNA structure. Sci Rep 2019; 9:14253. [PMID: 31582767 PMCID: PMC6776556 DOI: 10.1038/s41598-019-50211-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/05/2019] [Indexed: 01/02/2023] Open
Abstract
MC1, a monomeric nucleoid-associated protein (NAP), is structurally unrelated to other DNA-binding proteins. The protein participates in the genome organization of several Euryarchaea species through an atypical compaction mechanism. It is also involved in DNA transcription and cellular division through unknown mechanisms. We determined the 3D solution structure of a new DNA-protein complex formed by MC1 and a strongly distorted 15 base pairs DNA. While the protein just needs to adapt its conformation slightly, the DNA undergoes a dramatic curvature (the first two bend angles of 55° and 70°, respectively) and an impressive torsional stress (dihedral angle of 106°) due to several kinks upon binding of MC1 to its concave side. Thus, it adopts a V-turn structure. For longer DNAs, MC1 stabilizes multiple V-turn conformations in a flexible and dynamic manner. The existence of such V-turn conformations of the MC1-DNA complexes leads us to propose two binding modes of the protein, as a bender (primary binding mode) and as a wrapper (secondary binding mode). Moreover, it opens up new opportunities for studying and understanding the repair, replication and transcription molecular machineries of Archaea.
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Affiliation(s)
- Karine Loth
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France. .,UFR Collegium Sciences et Techniques, Université d'Orléans, rue de Chartres, 45100, Orléans, France.
| | - Justine Largillière
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France
| | - Franck Coste
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France
| | - Françoise Culard
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France
| | - Céline Landon
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France
| | - Agnès F Delmas
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France
| | - Françoise Paquet
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, rue Charles Sadron, F-45071, Orléans, Cedex 2, France.
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22
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Brunk CF, Martin WF. Archaeal Histone Contributions to the Origin of Eukaryotes. Trends Microbiol 2019; 27:703-714. [PMID: 31076245 DOI: 10.1016/j.tim.2019.04.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/01/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022]
Abstract
The eukaryotic lineage arose from bacterial and archaeal cells that underwent a symbiotic merger. At the origin of the eukaryote lineage, the bacterial partner contributed genes, metabolic energy, and the building blocks of the endomembrane system. What did the archaeal partner donate that made the eukaryotic experiment a success? The archaeal partner provided the potential for complex information processing. Archaeal histones were crucial in that regard by providing the basic functional unit with which eukaryotes organize DNA into nucleosomes, exert epigenetic control of gene expression, transcribe genes with CCAAT-box promoters, and a manifest cell cycle with condensed chromosomes. While mitochondrial energy lifted energetic constraints on eukaryotic protein production, histone-based chromatin organization paved the path to eukaryotic genome complexity, a critical hurdle en route to the evolution of complex cells.
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Affiliation(s)
- Clifford F Brunk
- Department of Ecology and Evolutionary Biology and Molecular Biology Institute University of California Los Angeles, Los Angeles, USA
| | - William F Martin
- Institute of Molecular Evolution Heinrich-Heine-Universitaet Duesseldorf, Dusseldorf, Germany.
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23
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Abstract
The genomes of all organisms throughout the tree of life are compacted and organized in chromatin by association of chromatin proteins. Eukaryotic genomes encode histones, which are assembled on the genome into octamers, yielding nucleosomes. Post-translational modifications of the histones, which occur mostly on their N-terminal tails, define the functional state of chromatin. Like eukaryotes, most archaeal genomes encode histones, which are believed to be involved in the compaction and organization of their genomes. Instead of discrete multimers, in vivo data suggest assembly of “nucleosomes” of variable size, consisting of multiples of dimers, which are able to induce repression of transcription. Based on these data and a model derived from X-ray crystallography, it was recently proposed that archaeal histones assemble on DNA into “endless” hypernucleosomes. In this review, we discuss the amino acid determinants of hypernucleosome formation and highlight differences with the canonical eukaryotic octamer. We identify archaeal histones differing from the consensus, which are expected to be unable to assemble into hypernucleosomes. Finally, we identify atypical archaeal histones with short N- or C-terminal extensions and C-terminal tails similar to the tails of eukaryotic histones, which are subject to post-translational modification. Based on the expected characteristics of these archaeal histones, we discuss possibilities of involvement of histones in archaeal transcription regulation. Both Archaea and eukaryotes express histones, but whereas the tertiary structure of histones is conserved, the quaternary structure of histone–DNA complexes is very different. In a recent study, the crystal structure of the archaeal hypernucleosome was revealed to be an “endless” core of interacting histones that wraps the DNA around it in a left-handed manner. The ability to form a hypernucleosome is likely determined by dimer–dimer interactions as well as stacking interactions between individual layers of the hypernucleosome. We analyzed a wide variety of archaeal histones and found that most but not all histones possess residues able to facilitate hypernucleosome formation. Among these are histones with truncated termini or extended histone tails. Based on our analysis, we propose several possibilities of archaeal histone involvement in transcription regulation.
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Affiliation(s)
- Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Clara van Emmerik
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Hugo van Ingen
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Remus T. Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
- * E-mail:
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24
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Bhattacharyya S, Mattiroli F, Luger K. Archaeal DNA on the histone merry-go-round. FEBS J 2018; 285:3168-3174. [PMID: 29729078 DOI: 10.1111/febs.14495] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/20/2018] [Accepted: 04/27/2018] [Indexed: 12/30/2022]
Abstract
How did the nucleosome, the fundamental building block of all eukaryotic chromatin, evolve? This central question has been impossible to address because the four core histones that make up the protein core of the nucleosome are so highly conserved in all eukaryotes. With the discovery of small, minimalist histone-like proteins in most known archaea, the likely origin of histones was identified. We recently determined the structure of an archaeal histone-DNA complex, revealing that archaeal DNA topology and protein-DNA interactions are astonishingly similar compared to the eukaryotic nucleosome. This was surprising since most archaeal histones form homodimers which consist only of the minimal histone fold and are devoid of histone tails and extensions. Unlike eukaryotic H2A-H2B and H3-H4 heterodimers that assemble into octameric particles wrapping ~ 150 bp DNA, archaeal histones form polymers around which DNA coils in a quasi-continuous superhelix. At any given point, this superhelix has the same geometry as nucleosomal DNA. This suggests that the architectural role of histones (i.e. the ability to bend DNA into a nucleosomal superhelix) was established before archaea and eukaryotes diverged, while the ability to form discrete particles, together with signaling functions of eukaryotic chromatin (i.e. epigenetic modifications) were secondary additions.
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Affiliation(s)
| | | | - Karolin Luger
- Howard Hughes Medical Institute, Boulder, CO, USA.,Department of Chemistry and Biochemistry, University of Colorado at Boulder, CO, USA
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25
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Koyama M, Kurumizaka H. Structural diversity of the nucleosome. J Biochem 2017; 163:85-95. [DOI: 10.1093/jb/mvx081] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 10/31/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
- Masako Koyama
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Institute for Medical-Oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Institute for Medical-Oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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26
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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: 82] [Impact Index Per Article: 9.1] [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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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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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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Close encounters of the third domain: the emerging genomic view of archaeal diversity and evolution. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:202358. [PMID: 24348093 PMCID: PMC3852633 DOI: 10.1155/2013/202358] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/21/2013] [Indexed: 01/06/2023]
Abstract
The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life.
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Periodic distribution of a putative nucleosome positioning motif in human, nonhuman primates, and archaea: mutual information analysis. Int J Genomics 2013; 2013:963956. [PMID: 23841049 PMCID: PMC3691935 DOI: 10.1155/2013/963956] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/29/2013] [Indexed: 12/12/2022] Open
Abstract
Recently, Trifonov's group proposed a 10-mer DNA motif YYYYYRRRRR as a solution of the long-standing problem of sequence-based nucleosome positioning. To test whether this generic decamer represents a biological meaningful signal, we compare the distribution of this motif in primates and Archaea, which are known to contain nucleosomes, and in Eubacteria, which do not possess nucleosomes. The distribution of the motif is analyzed by the mutual information function (MIF) with a shifted version of itself (MIF profile). We found common features in the patterns of this generic decamer on MIF profiles among primate species, and interestingly we found conspicuous but dissimilar MIF profiles for each Archaea tested. The overall MIF profiles for each chromosome in each primate species also follow a similar pattern. Trifonov's generic decamer may be a highly conserved motif for the nucleosome positioning, but we argue that this is not the only motif. The distribution of this generic decamer exhibits previously unidentified periodicities, which are associated to highly repetitive sequences in the genome. Alu repetitive elements contribute to the most fundamental structure of nucleosome positioning in higher Eukaryotes. In some regions of primate chromosomes, the distribution of the decamer shows symmetrical patterns including inverted repeats.
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Nalabothula N, Xi L, Bhattacharyya S, Widom J, Wang JP, Reeve JN, Santangelo TJ, Fondufe-Mittendorf YN. Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs. BMC Genomics 2013; 14:391. [PMID: 23758892 PMCID: PMC3691661 DOI: 10.1186/1471-2164-14-391] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 05/31/2013] [Indexed: 02/03/2023] Open
Abstract
Background Histone wrapping of DNA into nucleosomes almost certainly evolved in the Archaea, and predates Eukaryotes. In Eukaryotes, nucleosome positioning plays a central role in regulating gene expression and is directed by primary sequence motifs that together form a nucleosome positioning code. The experiments reported were undertaken to determine if archaeal histone assembly conforms to the nucleosome positioning code. Results Eukaryotic nucleosome positioning is favored and directed by phased helical repeats of AA/TT/AT/TA and CC/GG/CG/GC dinucleotides, and disfavored by longer AT-rich oligonucleotides. Deep sequencing of genomic DNA protected from micrococcal nuclease digestion by assembly into archaeal nucleosomes has established that archaeal nucleosome assembly is also directed and positioned by these sequence motifs, both in vivo in Methanothermobacter thermautotrophicus and Thermococcus kodakarensis and in vitro in reaction mixtures containing only one purified archaeal histone and genomic DNA. Archaeal nucleosomes assembled at the same locations in vivo and in vitro, with much reduced assembly immediately upstream of open reading frames and throughout the ribosomal rDNA operons. Providing further support for a common positioning code, archaeal histones assembled into nucleosomes on eukaryotic DNA and eukaryotic histones into nucleosomes on archaeal DNA at the same locations. T. kodakarensis has two histones, designated HTkA and HTkB, and strains with either but not both histones deleted grow normally but do exhibit transcriptome differences. Comparisons of the archaeal nucleosome profiles in the intergenic regions immediately upstream of genes that exhibited increased or decreased transcription in the absence of HTkA or HTkB revealed substantial differences but no consistent pattern of changes that would correlate directly with archaeal nucleosome positioning inhibiting or stimulating transcription. Conclusions The results obtained establish that an archaeal histone and a genome sequence together are sufficient to determine where archaeal nucleosomes preferentially assemble and where they avoid assembly. We confirm that the same nucleosome positioning code operates in Archaea as in Eukaryotes and presumably therefore evolved with the histone-fold mechanism of DNA binding and compaction early in the archaeal lineage, before the divergence of Eukaryotes.
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Affiliation(s)
- Narasimharao Nalabothula
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
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Alba shapes the archaeal genome using a delicate balance of bridging and stiffening the DNA. Nat Commun 2013; 3:1328. [PMID: 23271660 PMCID: PMC3535426 DOI: 10.1038/ncomms2330] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 11/26/2012] [Indexed: 11/29/2022] Open
Abstract
Architectural proteins have an important role in shaping the genome and act as global regulators of gene expression. How these proteins jointly modulate genome plasticity is largely unknown. In archaea, one of the most abundant proteins, Alba, is considered to have a key role in organizing the genome. Here we characterize the multimodal architectural properties and interplay of the Alba1 and Alba2 proteins using single-molecule imaging and manipulation techniques. We demonstrate that the two paralogues can bridge and rigidify DNA and that the interplay between the two proteins influences the balance between these effects. Our data yield a structural model that explains the multimodal behaviour of Alba proteins and its impact on genome folding. How the genome is physically organized is less understood in archaea than in eubacteria or eukaryotes. Laurens et al. measure DNA binding by the Sulfolobus solfataricus proteins Alba1 and Alba2 using single-molecule techniques and conclude that the presence of Alba2 leads to more bridging between DNA.
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Kumari S, Swaminathan A, Chatterjee S, Senapati P, Boopathi R, Kundu TK. Chromatin organization, epigenetics and differentiation: an evolutionary perspective. Subcell Biochem 2013; 61:3-35. [PMID: 23150244 DOI: 10.1007/978-94-007-4525-4_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Genome packaging is a universal phenomenon from prokaryotes to higher mammals. Genomic constituents and forces have however, travelled a long evolutionary route. Both DNA and protein elements constitute the genome and also aid in its dynamicity. With the evolution of organisms, these have experienced several structural and functional changes. These evolutionary changes were made to meet the challenging scenario of evolving organisms. This review discusses in detail the evolutionary perspective and functionality gain in the phenomena of genome organization and epigenetics.
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Affiliation(s)
- Sujata Kumari
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit (MBGU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Post, Bangalore, 560064, India
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An archaeal histone is required for transformation of Thermococcus kodakarensis. J Bacteriol 2012; 194:6864-74. [PMID: 23065975 DOI: 10.1128/jb.01523-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Archaeal histones wrap DNA into complexes, designated archaeal nucleosomes, that resemble the tetrasome core of a eukaryotic nucleosome. Therefore, all DNA interactions in vivo in Thermococcus kodakarensis, the most genetically versatile model species for archaeal research, must occur in the context of a histone-bound genome. Here we report the construction and properties of T. kodakarensis strains that have TK1413 or TK2289 deleted, the genes that encode HTkA and HTkB, respectively, the two archaeal histones present in this archaeon. All attempts to generate a strain with both TK1413 and TK2289 deleted were unsuccessful, arguing that a histone-mediated event(s) in T. kodakarensis is essential. The HTkA and HTkB amino acid sequences are 84% identical (56 of 67 residues) and 94% similar (63 of 67 residues), but despite this homology and their apparent redundancy in terms of supporting viability, the absence of HTkA and HTkB resulted in differences in growth and in quantitative and qualitative differences in genome transcription. A most surprising result was that the deletion of TK1413 (ΔhtkA) resulted in a T. kodakarensis strain that was no longer amenable to transformation, whereas the deletion of TK2289 (ΔhtkB) had no detrimental effects on transformation. Potential roles for the archaeal histones in regulating gene expression and for HTkA in DNA uptake and recombination are discussed.
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Huber E, Scharf D, Hortschansky P, Groll M, Brakhage A. DNA Minor Groove Sensing and Widening by the CCAAT-Binding Complex. Structure 2012; 20:1757-68. [DOI: 10.1016/j.str.2012.07.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 10/28/2022]
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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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A new fusion hypothesis for the origin of Eukarya: better than previous ones, but probably also wrong. Res Microbiol 2011; 162:77-91. [DOI: 10.1016/j.resmic.2010.10.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Anderson I, Djao ODN, Misra M, Chertkov O, Nolan M, Lucas S, Lapidus A, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Brambilla E, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Sikorski J, Spring S, Rohde M, Eichinger K, Huber H, Wirth R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Methanothermus fervidus type strain (V24S). Stand Genomic Sci 2010; 3:315-24. [PMID: 21304736 PMCID: PMC3035299 DOI: 10.4056/sigs.1283367] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Methanothermus fervidus Stetter 1982 is the type strain of the genus Methanothermus. This hyperthermophilic genus is of a thought to be endemic in Icelandic hot springs. M. fervidus was not only the first characterized organism with a maximal growth temperature (97°C) close to the boiling point of water, but also the first archaeon in which a detailed functional analysis of its histone protein was reported and the first one in which the function of 2,3-cyclodiphosphoglycerate in thermoadaptation was characterized. Strain V24S(T) is of interest because of its very low substrate ranges, it grows only on H(2) + CO(2). This is the first completed genome sequence of the family Methanothermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,243,342 bp long genome with its 1,311 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Transcriptional activation in the context of repression mediated by archaeal histones. Proc Natl Acad Sci U S A 2010; 107:6777-81. [PMID: 20351259 DOI: 10.1073/pnas.1002360107] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many archaea (including all the methanogens, nearly all euryarchaeotes, and some crenarchaeotes) use histones as components of the chromatin that compacts their genomes. The archaeal histones are homo- and heterodimers that pair on DNA to form tetrasomes (as the eukaryotic histones H3 and H4 do). The resulting DNA packaging is known to interfere with assembly of the archaeal transcription apparatus at promoters; the ability of transcriptional activation to function in repressive archaeal chromatin has not yet been explored in vitro. Using four of the Methanocaldococcus jannaschii (Mja) histones, we have examined activation of the model Mja rb2 transcription unit by the Mja transcriptional activator Ptr2 in this simplified-chromatin context. Using hydroxyl radical footprinting, we find that the Ptr2-specific rb2 upstream activating site is a preferred histone-localizing site that nucleates histone: DNA-binding radiating from the rb2 promoter. Nevertheless, Ptr2 competes effectively with histones for access to the rb2 promoter and most potently activates transcription in vitro at histone concentrations that extensively coat DNA and essentially silence basal transcription.
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Sequence Recognition of DNA by Protein-Induced Conformational Transitions. J Mol Biol 2010; 396:1145-64. [DOI: 10.1016/j.jmb.2009.12.050] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 12/23/2009] [Accepted: 12/25/2009] [Indexed: 11/21/2022]
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Modern Atomic Force Microscopy and Its Application to the Study of Genome Architecture. SCANNING PROBE MICROSCOPY IN NANOSCIENCE AND NANOTECHNOLOGY 2010. [DOI: 10.1007/978-3-642-03535-7_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Luijsterburg MS, White MF, van Driel R, Dame RT. The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit Rev Biochem Mol Biol 2009; 43:393-418. [PMID: 19037758 DOI: 10.1080/10409230802528488] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The genomic DNA of all organisms across the three kingdoms of life needs to be compacted and functionally organized. Key players in these processes are DNA supercoiling, macromolecular crowding and architectural proteins that shape DNA by binding to it. The architectural proteins in bacteria, archaea and eukaryotes generally do not exhibit sequence or structural conservation especially across kingdoms. Instead, we propose that they are functionally conserved. Most of these proteins can be classified according to their architectural mode of action: bending, wrapping or bridging DNA. In order for DNA transactions to occur within a compact chromatin context, genome organization cannot be static. Indeed chromosomes are subject to a whole range of remodeling mechanisms. In this review, we discuss the role of (i) DNA supercoiling, (ii) macromolecular crowding and (iii) architectural proteins in genome organization, as well as (iv) mechanisms used to remodel chromosome structure and to modulate genomic activity. We conclude that the underlying mechanisms that shape and remodel genomes are remarkably similar among bacteria, archaea and eukaryotes.
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Affiliation(s)
- Martijn S Luijsterburg
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan, Amsterdam, The Netherlands
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Eirín-López JM, González-Romero R, Dryhurst D, Méndez J, Ausió J. Long-Term Evolution of Histone Families: Old Notions and New Insights into Their Mechanisms of Diversification Across Eukaryotes. Evol Biol 2009. [DOI: 10.1007/978-3-642-00952-5_8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Guo L, Feng Y, Zhang Z, Yao H, Luo Y, Wang J, Huang L. Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea. Nucleic Acids Res 2008; 36:1129-37. [PMID: 18096617 PMCID: PMC2275093 DOI: 10.1093/nar/gkm1128] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 12/03/2007] [Accepted: 12/04/2007] [Indexed: 11/13/2022] Open
Abstract
Archaea contain a variety of chromatin proteins consistent with the evolution of different genome packaging mechanisms. Among the two main kingdoms in the Archaea, Euryarchaeota synthesize histone homologs, whereas Crenarchaeota have not been shown to possess a chromatin protein conserved at the kingdom level. We report the identification of Cren7, a novel family of chromatin proteins highly conserved in the Crenarchaeota. A small, basic, methylated and abundant protein, Cren7 displays a higher affinity for double-stranded DNA than for single-stranded DNA, constrains negative DNA supercoils and is associated with genomic DNA in vivo. The solution structure and DNA-binding surface of Cren7 from the hyperthermophilic crenarchaeon Sulfolobus solfataricus were determined by NMR. The protein adopts an SH3-like fold. It interacts with duplex DNA through a beta-sheet and a long flexible loop, presumably resulting in DNA distortions through intercalation of conserved hydrophobic residues into the DNA structure. These data suggest that the crenarchaeal kingdom in the Archaea shares a common strategy in chromatin organization.
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Affiliation(s)
- Li Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Yingang Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Zhenfeng Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Hongwei Yao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Yuanming Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Jinfeng Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
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Weidenbach K, Glöer J, Ehlers C, Sandman K, Reeve JN, Schmitz RA. Deletion of the archaeal histone in Methanosarcina mazei Gö1 results in reduced growth and genomic transcription. Mol Microbiol 2007; 67:662-71. [PMID: 18086209 DOI: 10.1111/j.1365-2958.2007.06076.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
HMm is the only archaeal histone in Methanosarcina mazei Göl and recombinant HMm, synthesized by expression of MM1825 in Escherichia coli, has been purified and confirmed to have the DNA binding and compaction properties characteristic of an archaeal histone. Insertion of a puromycin resistance conferring cassette (pac) into MM1825 was not lethal but resulted in mutants (M. mazei MM1825::pac) that have impaired ability to grow on methanol and trimethylamine. Loss of HMm also resulted in increased sensitivity to UV light and decreased transcript levels for approximately 25% of all M. mazei genes. For most genes, the transcript decrease was 3- to 10-fold, but transcripts of MM483 (small heat-shock protein), MM1688 (trimethylamine:corrinoid methyl transferase) and MM3195 (transcription regulator), were reduced 100-, 100- and 25-fold, respectively, in M. mazei MM1825::pac cells. Transcripts of only five adjacent genes that appear to constitute an aromatic amino acid biosynthetic operon were elevated in M. mazei MM1825::pac cells. Complementary synthesis of HMm from a plasmid transformed into M. mazei MM1825::pac restored wild-type growth and transcript levels.
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Affiliation(s)
- Katrin Weidenbach
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
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Mayer F. Cytoskeletal Elements in Bacteria Mycoplasma pneumoniae, Thermoanaerobacterium sp., and Escherichia coli as Revealed by Electron Microscopy. J Mol Microbiol Biotechnol 2006; 11:228-43. [PMID: 16983198 DOI: 10.1159/000094057] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recently, electron microscopic studies on the eubacteria Mycoplasma pneumoniae, Thermoanaerobacterium sp., and Escherichia coli have revealed the existence of cytoskeletal elements so far unknown in prokaryotes. The wall-less bacterium M. pneumoniae contains, in close vicinity to the inner face of the cytoplasmic membrane, a helically organized lining composed of protein elements that form a regular network of meshes that encloses the entire cytoplasm. Numerous regularly spaced pin-like structural elements, the stalks with terminal knobs, connect the lining with the cytoplasmic membrane. In this bacterium, a specific rod-like structural element is located in the tip region. Occasionally, it is bent or twisted. It consists of two matching blade-like sub-elements. A number of parallel linkers, extending from the edges of the rod, make contact with the lining. The proximal end of the rod is attached to a wheel-like complex. Fibrils originating from the wheel cross the cytoplasm and make contact with the lining. E. coli contains a similar helically organized lining close to the inner face of the cytoplasmic membrane. Groups of ribosomes (polysomes) were seen to be attached to the helical elements of the lining. A feature that is common to both bacteria and to Thermoanaerobacterium sp. appears to be that the lining and the fibrils crossing the cytoplasm contain a high number of copies of the bacterial elongation factor Tu (EF-Tu). This indicates that this protein may play an important role as a structural element in bacterial cytoskeletons. This notion was supported by experiments in which the cytoskeleton in E. coli was destabilized by induced expression of truncated EF-Tu, with the consequence of cell lysis, and by the finding that in vitro polymerization of monomeric EF-Tu into protofilaments was hindered in a mixture of full-size EF-Tu and truncated EF-Tu consisting of domain 3 only. Current research and developmental efforts are aimed at the design of a new class of antibacterial drugs, acting by destabilization of the EF-Tu-containing bacterial cytoskeleton, and of an innovative mode of inducible lysis of recombinant bacteria by controlled destabilization of the EF-Tu-containing cytoskeleton.
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Affiliation(s)
- Frank Mayer
- Institut fur Mikrobiologie und Genetik, Georg-August-Universitat Gottingen, Gottingen, Germany.
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Qiu Y, Tereshko V, Kim Y, Zhang R, Collart F, Yousef M, Kossiakoff A, Joachimiak A. The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold. Proteins 2006; 62:8-16. [PMID: 16287087 PMCID: PMC2792020 DOI: 10.1002/prot.20590] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The structure of Aq_328, an uncharacterized protein from hyperthermophilic bacteria Aquifex aeolicus, has been determined to 1.9 A by using multi-wavelength anomalous diffraction (MAD) phasing. Although the amino acid sequence analysis shows that Aq_328 has no significant similarity to proteins with a known structure and function, the structure comparison by using the Dali server reveals that it: (1) assumes a histone-like fold, and (2) is similar to an ancestral nuclear histone protein (PDB code 1F1E) with z-score 8.1 and RMSD 3.6 A over 124 residues. A sedimentation equilibrium experiment indicates that Aq_328 is a monomer in solution, with an average sedimentation coefficient of 2.4 and an apparent molecular weight of about 20 kDa. The overall architecture of Aq_328 consists of two noncanonical histone domains in tandem repeat within a single chain, and is similar to eukaryotic heterodimer (H2A/H2B and H3/H4) and an archaeal histone heterodimer (HMfA/HMfB). The sequence comparisons between the two histone domains of Aq_328 and six eukaryotic/archaeal histones demonstrate that most of the conserved residues that underlie the Aq_328 architecture are used to build and stabilize the two cross-shaped antiparallel histone domains. The high percentage of salt bridges in the structure could be a factor in the protein's thermostability. The structural similarities to other histone-like proteins, molecular properties, and potential function of Aq_328 are discussed in this paper.
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Affiliation(s)
- Yang Qiu
- The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Valentina Tereshko
- The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Youngchang Kim
- Structural Biology Center and Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois
| | - Rongguang Zhang
- Structural Biology Center and Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois
| | - Frank Collart
- Structural Biology Center and Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois
| | - Mohammed Yousef
- The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Anthony Kossiakoff
- The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Andrzej Joachimiak
- The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
- Structural Biology Center and Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois
- Correspondence to: Andrzej Joachimiak, Structural Biology Center and Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, Illinois 60439. and Anthony Kossia-koff, The University of Chicago, Department of Biochemistry and Molecular Biology, University of Chicago, 920 E. 58 St., Chicago, IL 60637.
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Abstract
One of the first hurdles to be negotiated in the postgenomic era involves the description of the entire protein content of the cell, the proteome. Such efforts are presently complicated by the various posttranslational modifications that proteins can experience, including glycosylation, lipid attachment, phosphorylation, methylation, disulfide bond formation, and proteolytic cleavage. Whereas these and other posttranslational protein modifications have been well characterized in Eucarya and Bacteria, posttranslational modification in Archaea has received far less attention. Although archaeal proteins can undergo posttranslational modifications reminiscent of what their eucaryal and bacterial counterparts experience, examination of archaeal posttranslational modification often reveals aspects not previously observed in the other two domains of life. In some cases, posttranslational modification allows a protein to survive the extreme conditions often encountered by Archaea. The various posttranslational modifications experienced by archaeal proteins, the molecular steps leading to these modifications, and the role played by posttranslational modification in Archaea form the focus of this review.
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Affiliation(s)
- Jerry Eichler
- Dept. of Life Sciences, Ben Gurion University, P.O. Box 653, Beersheva 84105, Israel.
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50
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Marsh VL, Peak-Chew SY, Bell SD. Sir2 and the Acetyltransferase, Pat, Regulate the Archaeal Chromatin Protein, Alba. J Biol Chem 2005; 280:21122-8. [PMID: 15824122 DOI: 10.1074/jbc.m501280200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DNA binding affinity of Alba, a chromatin protein of the archaeon Sulfolobus solfataricus P2, is regulated by acetylation of lysine 16. Here we identify an acetyltransferase that specifically acetylates Alba on this residue. The effect of acetylation is to lower the affinity of Alba for DNA. Remarkably, the acetyltransferase is conserved not only in archaea but also in bacteria where it appears to play a role in metabolic regulation. Therefore, our data suggest that S. solfataricus has co-opted this bacterial regulatory system to generate a rudimentary form of chromatin regulation.
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Affiliation(s)
- Victoria L Marsh
- Medical Research Council Cancer Cell Unit, Hutchison Medical Research Council Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
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