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Gandhivel VHS, Sotelo-Parrilla P, Raju S, Jha S, Gireesh A, Harshith CY, Gut F, Vinothkumar KR, Berger F, Jeyaprakash AA, Shivaprasad P. An Oryza-specific histone H4 variant predisposes H4 lysine 5 acetylation to modulate salt stress responses. NATURE PLANTS 2025; 11:790-807. [PMID: 40200022 PMCID: PMC7617672 DOI: 10.1038/s41477-025-01974-2] [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] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 03/04/2025] [Indexed: 04/10/2025]
Abstract
Paralogous variants of canonical histones guide accessibility to DNA and function as additional layers of genome regulation. Across eukaryotes, the mechanism of action and functional significance of several variants of core histones are well known except those of histone H4. Here we show that a variant of H4 (H4.V) expressing tissue-specifically among Oryza members mediated specific epigenetic changes contributing to salt tolerance. H4.V was incorporated into specific heterochromatic sites, where it blocked the deposition of active histone marks. Stress-dependent redistribution of H4.V enabled the incorporation of acetylated H4 lysine 5 (H4K5ac) in the gene bodies. The misexpression of H4.V led to defects in reproductive development and in mounting salt stress responses. H4.V formed homotypic nucleosomes and mediated these alterations by conferring distinct molecular properties to the nucleosomes, as seen with cryo electron microscopy structures and biochemical assays. These results reveal not only an H4 variant among plants but also a chromatin regulation that might have contributed to the adaptation of semi-aquatic Oryza members.
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Affiliation(s)
| | - Paula Sotelo-Parrilla
- Gene Center and Department of Biochemistry, Ludwig-Maximilian-Universität, München, Feodor-Lynen Straße 25, 81377Munich, Germany
| | - Steffi Raju
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur613 401, India
| | - Shaileshanand Jha
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore560065, India
| | - Anjitha Gireesh
- Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 BFUK
| | | | - Fabian Gut
- Gene Center and Department of Biochemistry, Ludwig-Maximilian-Universität, München, Feodor-Lynen Straße 25, 81377Munich, Germany
| | - Kutti R. Vinothkumar
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore560065, India
| | - Frédéric Berger
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 31030, Vienna, Austria
| | - A. Arockia Jeyaprakash
- Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 BFUK
- Gene Center and Department of Biochemistry, Ludwig-Maximilian-Universität, München, Feodor-Lynen Straße 25, 81377Munich, Germany
| | - P.V. Shivaprasad
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore560065, India
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2
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Nakabayashi Y, Seki M. A hypothesis for nucleosome evolution based on mutational analysis. Genes Genet Syst 2025; 100:n/a. [PMID: 39694494 DOI: 10.1266/ggs.24-00143] [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: 12/20/2024] Open
Abstract
Nucleosomes are complexes of DNA and histone proteins that form the basis of eukaryotic chromatin. Eukaryotic histones are descended from archaeal homologs; however, how this occurred remains unclear. Our previous genetic analysis of the budding yeast nucleosome identified 26 histone residues conserved between Saccharomyces cerevisiae and Trypanosoma brucei: 15 that are lethal when mutated and 11 that are synthetically lethal with deletion of the FEN1 nuclease. These residues are partially conserved in nucleosomes of a variety of giant viruses, allowing us to follow the route by which they were established in the LECA (last eukaryotic common ancestor). We analyzed yeast nucleosome genetic data to generate a model for the emergence of the eukaryotic nucleosome. In our model, histone H2B-H2A and H4-H3 doublets found in giant virus nucleosomes facilitated the formation of the acidic patch surface and nucleosome entry sites of the eukaryotic nucleosome, respectively. Splitting of the H2B-H2A doublet resulted in the H2A variant H2A.Z, and subsequent splitting of the H4-H3 doublet led to a eukaryote-specific domain required for chromatin binding of H2A.Z. We propose that the LECA emerged when the newly split H3 N-terminus horizontally acquired a common N-tail found in extinct pre-LECA lineages and some extant giant viruses. This hypothesis predicts that the emergence of the H3 variant CENP-A and the establishment of CENP-A-dependent chromosome segregation occurred after the emergence of the LECA, implying that the root of all eukaryotes is assigned within Euglenida.
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Affiliation(s)
- Yu Nakabayashi
- Division of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University
| | - Masayuki Seki
- Division of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University
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3
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Blombach F, Werner F. Chromatin and gene regulation in archaea. Mol Microbiol 2025; 123:218-231. [PMID: 39096085 PMCID: PMC11894787 DOI: 10.1111/mmi.15302] [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: 05/21/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 08/04/2024]
Abstract
The chromatinisation of DNA by nucleoid-associated proteins (NAPs) in archaea 'formats' the genome structure in profound ways, revealing both striking differences and analogies to eukaryotic chromatin. However, the extent to which archaeal NAPs actively regulate gene expression remains poorly understood. The dawn of quantitative chromatin mapping techniques and first NAP-specific occupancy profiles in different archaea promise a more accurate view. A picture emerges where in diverse archaea with very different NAP repertoires chromatin maintains access to regulatory motifs including the gene promoter independently of transcription activity. Our re-analysis of genome-wide occupancy data of the crenarchaeal NAP Cren7 shows that these chromatin-free regions are flanked by increased Cren7 binding across the transcription start site. While bacterial NAPs often form heterochromatin-like regions across islands with xenogeneic genes that are transcriptionally silenced, there is little evidence for similar structures in archaea and data from Haloferax show that the promoters of xenogeneic genes remain accessible. Local changes in chromatinisation causing wide-ranging effects on transcription restricted to one chromosomal interaction domain (CID) in Saccharolobus islandicus hint at a higher-order level of organisation between chromatin and transcription. The emerging challenge is to integrate results obtained at microscale and macroscale, reconciling molecular structure and function with dynamic genome-wide chromatin landscapes.
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Affiliation(s)
- Fabian Blombach
- Division of Biosciences, RNAP Laboratory, Institute of Structural and Molecular Biology (ISMB)University College LondonLondonUK
| | - Finn Werner
- Division of Biosciences, RNAP Laboratory, Institute of Structural and Molecular Biology (ISMB)University College LondonLondonUK
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4
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Villain P, Basta T. Regulation of DNA Topology in Archaea: State of the Art and Perspectives. Mol Microbiol 2025; 123:245-264. [PMID: 39709598 PMCID: PMC11894792 DOI: 10.1111/mmi.15328] [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: 05/03/2024] [Revised: 10/22/2024] [Accepted: 10/23/2024] [Indexed: 12/24/2024]
Abstract
DNA topology is a direct consequence of the double helical nature of DNA and is defined by how the two complementary DNA strands are intertwined. Virtually every reaction involving DNA is influenced by DNA topology or has topological effects. It is therefore of fundamental importance to understand how this phenomenon is controlled in living cells. DNA topoisomerases are the key actors dedicated to the regulation of DNA topology in cells from all domains of life. While significant progress has been made in the last two decades in understanding how these enzymes operate in vivo in Bacteria and Eukaryotes, studies in Archaea have been lagging behind. This review article aims to summarize what is currently known about DNA topology regulation by DNA topoisomerases in main archaeal model organisms. These model archaea exhibit markedly different lifestyles, genome organization and topoisomerase content, thus highlighting the diversity and the complexity of DNA topology regulation mechanisms and their evolution in this domain of life. The recent development of functional genomic assays supported by next-generation sequencing now allows to delve deeper into this timely and exciting, yet still understudied topic.
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Affiliation(s)
- Paul Villain
- Medical Research Council Laboratory of Medical SciencesLondonUK
- Institute of Clinical Sciences, Faculty of MedicineImperial College LondonLondonUK
| | - Tamara Basta
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
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5
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Schwab S, Dame RT. Identification, characterization and classification of prokaryotic nucleoid-associated proteins. Mol Microbiol 2025; 123:206-217. [PMID: 39039769 PMCID: PMC11894785 DOI: 10.1111/mmi.15298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [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 ChemistryLeiden UniversityLeidenThe Netherlands
- Centre for Microbial Cell BiologyLeiden UniversityLeidenThe Netherlands
- Centre for Interdisciplinary Genome ResearchLeiden UniversityLeidenThe Netherlands
| | - Remus T. Dame
- Leiden Institute of ChemistryLeiden UniversityLeidenThe Netherlands
- Centre for Microbial Cell BiologyLeiden UniversityLeidenThe Netherlands
- Centre for Interdisciplinary Genome ResearchLeiden UniversityLeidenThe Netherlands
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6
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Marinov GK, Doughty B, Kundaje A, Greenleaf WJ. The chromatin landscape of the histone-possessing Bacteriovorax bacteria. Genome Res 2025; 35:109-123. [PMID: 39572228 PMCID: PMC11789641 DOI: 10.1101/gr.279418.124] [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: 03/29/2024] [Accepted: 11/19/2024] [Indexed: 01/24/2025]
Abstract
Histone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, histone proteins have recently been identified in a few bacterial clades, most notably the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared with histones in archaea and eukaryotes. However, no functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription, and three-dimensional (3D) genome organization in a member of Bdellovibrionota (a Bacteriovorax strain). We find that, similar to what is observed in some archaea and in eukaryotes with compact genomes such as yeast, Bacteriovorax chromatin is characterized by preferential accessibility around promoter regions. Similar to eukaryotes, chromatin accessibility in Bacteriovorax positively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that unlike in yeast, but similar to the state of mammalian and fly promoters, Bacteriovorax promoters exhibit very strong polymerase pausing. Finally, similar to that of other bacteria without histones, the Bacteriovorax genome exists in a 3D configuration organized by the parABS system along the axis defined by replication origin and termination regions. These results provide a foundation for understanding the chromatin biology of the unique Bdellovibrionota bacteria and the functional diversity in chromatin organization across the tree of life.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, California 94305, USA;
| | - Benjamin Doughty
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Arc Institute, Palo Alto, California 94304, USA
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7
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Ren Z, Way LE, Wang X. SMC translocation is unaffected by an excess of nucleoid associated proteins in vivo. Sci Rep 2025; 15:2447. [PMID: 39828741 PMCID: PMC11743769 DOI: 10.1038/s41598-025-86946-4] [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: 10/31/2024] [Accepted: 01/15/2025] [Indexed: 01/22/2025] Open
Abstract
Genome organization is important for DNA replication, gene expression, and chromosome segregation. In bacteria, two large families of proteins, nucleoid-associated proteins (NAPs) and SMC complexes, play important roles in organizing the genome. NAPs are highly abundant DNA-binding proteins that can bend, wrap, bridge, and compact DNA, while SMC complexes load onto the chromosome, translocate on the DNA, and extrude DNA loops. Although SMC complexes are capable of traversing the entire chromosome bound by various NAPs in vivo, it is unclear whether SMC translocation is influenced by NAPs. In this study, using Bacillus subtilis as a model system, we expressed a collection of representative bacterial and archaeal DNA-binding proteins that introduce distinct DNA structures and potentially pose different challenges for SMC movement. By fluorescence microscopy and chromatin immunoprecipitation, we observed that these proteins bound to the genome in characteristic manners. Using genome-wide chromosome conformation capture (Hi-C) assays, we found that the SMC complex traversed these DNA-binding proteins without slowing down. Our findings revealed that the DNA-loop-extruding activity of the SMC complex is unaffected by exogenously expressed DNA-binding proteins, which highlights the robustness of SMC motors on the busy chromatin.
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Affiliation(s)
- Zhongqing Ren
- Department of Biology, Indiana University, 1001 E 3rd Street, Bloomington, IN 47405, USA
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lindsey E Way
- Department of Biology, Indiana University, 1001 E 3rd Street, Bloomington, IN 47405, USA
| | - Xindan Wang
- Department of Biology, Indiana University, 1001 E 3rd Street, Bloomington, IN 47405, USA.
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8
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Timsit Y. The Expanding Universe of Extensions and Tails: Ribosomal Proteins and Histones in RNA and DNA Complex Signaling and Dynamics. Genes (Basel) 2025; 16:45. [PMID: 39858592 PMCID: PMC11764897 DOI: 10.3390/genes16010045] [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] [Received: 12/09/2024] [Revised: 12/26/2024] [Accepted: 12/27/2024] [Indexed: 01/27/2025] Open
Abstract
This short review bridges two biological fields: ribosomes and nucleosomes-two nucleoprotein assemblies that, along with many viruses, share proteins featuring long filamentous segments at their N- or C-termini. A central hypothesis is that these extensions and tails perform analogous functions in both systems. The evolution of these structures appears closely tied to the emergence of regulatory networks and signaling pathways, facilitating increasingly complex roles for ribosomes and nucleosome alike. This review begins by summarizing the structures and functions of ribosomes and nucleosomes, followed by a detailed comparison highlighting their similarities and differences, particularly in light of recent findings on the roles of ribosomal proteins in signaling and ribosome dynamics. The analysis seeks to uncover whether these systems operate based on shared principles and mechanisms. The nucleosome-ribosome analogy may offer valuable insights into unresolved questions in both fields. For instance, new structural insights from ribosomes might shed light on potential motifs formed by histone tails. From an evolutionary perspective, this study revisits the origins of signaling and regulation in ancient nucleoprotein assemblies, suggesting that tails and extensions may represent remnants of the earliest network systems governing signaling and dynamic control.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France;
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Rue Michel-Ange, 75016 Paris, France
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9
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Ali-Ahmad A, Mors M, Carrer M, Li X, Bilokapić S, Halić M, Cascella M, Sekulić N. Non-nucleosomal (CENP-A/H4) 2 - DNA complexes as a possible platform for centromere organization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.12.31.630874. [PMID: 39803555 PMCID: PMC11722257 DOI: 10.1101/2024.12.31.630874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2025]
Abstract
The centromere is a part of the chromosome that is essential for the even segregation of duplicated chromosomes during cell division. It is epigenetically defined by the presence of the histone H3 variant CENP-A. CENP-A associates specifically with a group of 16 proteins that form the centromere-associated network of proteins (CCAN). In mitosis, the kinetochore forms on the CCAN to connect the duplicated chromosomes to the microtubules protruding from the cell poles. Previous studies have shown that CENP-A replaces H3 in nucleosomes, and recently the structures of CENP-A-containing nucleosomes in complex with CCANs have been revealed, but they show only a limited interaction between CCANs and CENP-A. Here, we report the cryoEM structure of 2x(CENP-A/H4)2-di-tetramers assembled on DNA in the absence of H2A/H2B histone dimer and speculate how (CENP-A/H4)2-tetramers and -di-tetramers might serve as a platform for CCAN organization.
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Affiliation(s)
- Ahmad Ali-Ahmad
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of Medicine, University of Oslo, Oslo 0318, Norway
| | - Mira Mors
- Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern 0315, Norway
| | - Manuel Carrer
- Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern 0315, Norway
| | - Xinmeng Li
- Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern 0315, Norway
| | - Silvija Bilokapić
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Mario Halić
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Michele Cascella
- Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern 0315, Norway
- Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Nikolina Sekulić
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of Medicine, University of Oslo, Oslo 0318, Norway
- Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern 0315, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
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10
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Yoshimura A, Seki M. The Possible Crystallization Process in the Origin of Bacteria, Archaea, Viruses, and Mobile Elements. BIOLOGY 2024; 14:3. [PMID: 39857234 PMCID: PMC11763024 DOI: 10.3390/biology14010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 12/03/2024] [Accepted: 12/18/2024] [Indexed: 01/27/2025]
Abstract
We propose a hypothesis for the simultaneous emergence of bacteria, archaea, viruses, and mobile elements by sequential and concrete biochemical pathways. The emergence process can be considered analogous to crystallization, where genetic and biochemical systems stabilize as organisms evolve from their common ancestor, the LUCA, which was a non-free-living pool of single operon type genomes including double-stranded (ds) DNA at an ancient submarine alkaline vent. Each dsDNA operon was transcribed by different systems in σ, TFIIB, or TBP genomes. Double-stranded DNA operons can fuse and stabilize through the action of specific transcription systems, leading to differentiation between the Bacteria (σ genome) and Archaea (TBP genome) domains. Error catastrophe can be overcome by the parallel gain of DNA replication and DNA repair mechanisms in both genomes. Enlarged DNA enabled efficient local biochemical reactions. Both genomes independently recruited lipids to facilitate reactions by forming coacervates at the chamber of the vent. Bilayer lipid membrane formation, proto-cell formation with a permeable membrane, proto-cell division, and the evolution of membrane-associated biochemistry are presented in detail. Simultaneous crystallization of systems in non-free-living bacteria and non-free-living archaea triggered the co-crystallization of primitive viruses and mobile elements. An arms race between non-free-living cells and primitive viruses finally led to free-living cells with a cell wall and mature viruses.
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Affiliation(s)
| | - Masayuki Seki
- Division of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai 981-8558, Japan;
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11
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Zhou X, Zhang N, Gong J, Zhang K, Chen P, Cheng X, Ye BC, Zhao G, Jing X, Li X. In vivo assembly of complete eukaryotic nucleosomes and (H3-H4)-only non-canonical nucleosomal particles in the model bacterium Escherichia coli. Commun Biol 2024; 7:1510. [PMID: 39543208 PMCID: PMC11564532 DOI: 10.1038/s42003-024-07211-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 11/04/2024] [Indexed: 11/17/2024] Open
Abstract
As a fundamental unit for packaging genomic DNA into chromatin, the eukaryotic nucleosome core comprises a canonical octamer with two copies for each histone, H2A, H2B, H3, and H4, wrapped around with 147 base pairs of DNA. While H3 and H4 share structure-fold with archaeal histone-like proteins, the eukaryotic nucleosome core and the complete nucleosome (the core plus H1 histone) are unique to eukaryotes. To explore whether the eukaryotic nucleosome can assemble in prokaryotes and to reconstruct the possible route for its emergence in eukaryogenesis, we developed an in vivo system for assembly of nucleosomes in the model bacterium, Escherichia coli, and successfully reconstituted the core nucleosome, the complete nucleosome, and unexpectedly the non-canonical (H3-H4)4 octasome. The core and complete nucleosomes assembled in E. coli exhibited footprints typical of eukaryotic hosts after in situ micrococcal nuclease digestion. Additionally, they caused condensation of E. coli nucleoid. We also demonstrated the stable formation of non-canonical (H3-H4)2 tetrasome and (H3-H4)4 octasomes in vivo, which are suggested to be 'fossil complex' that marks the intermediate in the progressive development of eukaryotic nucleosome. The study presents a unique platform in a bacterium for in vivo assembly and studying the properties of non-canonical variants of nucleosome.
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Affiliation(s)
- Xiaojuan Zhou
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
| | - Niubing Zhang
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jie Gong
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
| | - Kaixiang Zhang
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ping Chen
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiang Cheng
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
| | - Bang-Ce Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China.
| | - Xinyun Jing
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- University of Chinese Academy of Sciences, 100039, Beijing, China.
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12
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Toner CM, Hoitsma NM, Weerawarana S, Luger K. Characterization of Medusavirus encoded histones reveals nucleosome-like structures and a unique linker histone. Nat Commun 2024; 15:9138. [PMID: 39443461 PMCID: PMC11500106 DOI: 10.1038/s41467-024-53364-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 10/08/2024] [Indexed: 10/25/2024] Open
Abstract
The organization of DNA into nucleosomes is a ubiquitous and ancestral feature that was once thought to be exclusive to the eukaryotic domain of life. Intriguingly, several representatives of the Nucleocytoplasmic Large DNA Viruses (NCLDV) encode histone-like proteins that in Melbournevirus were shown to form nucleosome-like particles. Medusavirus medusae (MM), a distantly related giant virus, encodes all four core histone proteins and, unique amongst most giant viruses, a putative acidic protein with two domains resembling eukaryotic linker histone H1. Here, we report the structure of nucleosomes assembled with MM histones and highlight similarities and differences with eukaryotic and Melbournevirus nucleosomes. Our structure provides insight into how variations in histone tail and loop lengths are accommodated within the context of the nucleosome. We show that MM-histones assemble into tri-nucleosome arrays, and that the putative linker histone H1 does not function in chromatin compaction. These findings expand our limited understanding of chromatin organization by virus-encoded histones.
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Affiliation(s)
- Chelsea M Toner
- Department of Biochemistry, University of Colorado at Boulder, 80309, Boulder, CO, USA
| | - Nicole M Hoitsma
- Department of Biochemistry, University of Colorado at Boulder, 80309, Boulder, CO, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sashi Weerawarana
- Department of Biochemistry, University of Colorado at Boulder, 80309, Boulder, CO, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado at Boulder, 80309, Boulder, CO, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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13
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Povolotsky TL, Levy Barazany H, Shacham Y, Kolodkin-Gal I. Bacterial epigenetics and its implication for agriculture, probiotics development, and biotechnology design. Biotechnol Adv 2024; 75:108414. [PMID: 39019123 DOI: 10.1016/j.biotechadv.2024.108414] [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] [Received: 05/04/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024]
Abstract
In their natural habitats, organisms encounter numerous external stimuli and must be able to sense and adapt to those stimuli to survive. Unlike mutations, epigenetic changes do not alter the underlying DNA sequence. Instead, they create modifications that promote or silence gene expression. Bacillus subtilis has long been a model organism in studying genetics and development. It is beneficial for numerous biotechnological applications where it is included as a probiotic, in fermentation, or in bio-concrete design. This bacterium has also emerged recently as a model organism for studying bacterial epigenetic adaptation. In this review, we examine the evolving knowledge of epigenetic regulation (restriction-modification systems (RM), orphan methyltransferases, and chromosome condensation) in B. subtilis and related bacteria, and utilize it as a case study to test their potential roles and future applications in genetic engineering and microbial biotechnology. Finally, we suggest how the implementation of these fundamental findings promotes the design of synthetic epigenetic memory circuits and their future applications in agriculture, medicine, and biotechnology.
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Affiliation(s)
- Tatyana L Povolotsky
- Institute for Chemistry and Biochemistry, Physical and Theoretical Chemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195 Berlin, Germany
| | - Hilit Levy Barazany
- Scojen Institute for Synthetic Biology, Reichman University, Hauniversita 8, Herzeliya, Israel
| | - Yosi Shacham
- Scojen Institute for Synthetic Biology, Reichman University, Hauniversita 8, Herzeliya, Israel
| | - Ilana Kolodkin-Gal
- Scojen Institute for Synthetic Biology, Reichman University, Hauniversita 8, Herzeliya, Israel.
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14
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Jing X, Zhang N, Zhou X, Chen P, Gong J, Zhang K, Wu X, Cai W, Ye BC, Hao P, Zhao GP, Yang S, Li X. Creating a bacterium that forms eukaryotic nucleosome core particles. Nat Commun 2024; 15:8283. [PMID: 39333491 PMCID: PMC11436726 DOI: 10.1038/s41467-024-52484-2] [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: 06/15/2024] [Accepted: 09/10/2024] [Indexed: 09/29/2024] Open
Abstract
The nucleosome is one of the hallmarks of eukaryotes, a dynamic platform that supports many critical functions in eukaryotic cells. Here, we engineer the in vivo assembly of the nucleosome core in the model bacterium Escherichia coli. We show that bacterial chromosome DNA and eukaryotic histones can assemble in vivo to form nucleosome complexes with many features resembling those found in eukaryotes. The formation of nucleosomes in E. coli was visualized with atomic force microscopy and using tripartite split green fluorescent protein. Under a condition that moderate histones expression was induced at 1 µM IPTG, the nucleosome-forming bacterium is viable and has sustained growth for at least 110 divisions in longer-term growth experiments. It exhibits stable nucleosome formation, a consistent transcriptome across passages, and reduced growth fitness under stress conditions. In particular, the nucleosome arrays in E. coli genic regions have profiles resembling those in eukaryotic cells. The observed compatibility between the eukaryotic nucleosome and the bacterial chromosome machinery may reflect a prerequisite for bacteria-archaea union, providing insight into eukaryogenesis and the origin of the nucleosome.
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Grants
- This work was supported in part by the National Natural Science Foundation of China (32393971 awarded to X.J., 92451303 and 32270719 awarded to X.L., 32200093 awarded to P.C.), the National Key R&D Program of China (2023ZD04073 awarded to X.L.), the National Science and Technology Major Projects (2018YFA0903700 awarded to X.J., 2019YFA0904600 awarded to Yan Zhu), and the Strategic Projects of the Chinese Academy of Sciences (XDA24010403 awarded to X.L.). We thank Fan Gong at the National Facility for Protein Science in Shanghai (NFPS), Shanghai Advanced Research Institute, CAS, for technical support with AFM experiments, and Yuan Yuan Gao, Shanshan Wang, Lianyan Jing, and Xiaoyan Xu at the core facility of the Center for Excellence in Molecular Plant Sciences (CEMPS) for assistance with LC-MS/MS experiments.
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Affiliation(s)
- Xinyun Jing
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Niubing Zhang
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiaojuan Zhou
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ping Chen
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jie Gong
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kaixiang Zhang
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xueting Wu
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenjuan Cai
- Core Facility Center, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bang-Ce Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Pei Hao
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Guo-Ping Zhao
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
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15
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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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16
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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 PMCID: PMC11352870 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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17
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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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18
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Hustmyer CM, Landick R. Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression. Mol Microbiol 2024; 122:81-112. [PMID: 38847475 PMCID: PMC11260248 DOI: 10.1111/mmi.15283] [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: 01/11/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
DNA in bacterial chromosomes is organized into higher-order structures by DNA-binding proteins called nucleoid-associated proteins (NAPs) or bacterial chromatin proteins (BCPs). BCPs often bind to or near DNA loci transcribed by RNA polymerase (RNAP) and can either increase or decrease gene expression. To understand the mechanisms by which BCPs alter transcription, one must consider both steric effects and the topological forces that arise when DNA deviates from its fully relaxed double-helical structure. Transcribing RNAP creates DNA negative (-) supercoils upstream and positive (+) supercoils downstream whenever RNAP and DNA are unable to rotate freely. This (-) and (+) supercoiling generates topological forces that resist forward translocation of DNA through RNAP unless the supercoiling is constrained by BCPs or relieved by topoisomerases. BCPs also may enhance topological stress and overall can either inhibit or aid transcription. Here, we review current understanding of how RNAP, BCPs, and DNA topology interplay to control gene expression.
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Affiliation(s)
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison
- Department of Bacteriology, University of Wisconsin-Madison
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19
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Irwin NAT, Richards TA. Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes. Nat Microbiol 2024; 9:1713-1724. [PMID: 38806669 PMCID: PMC11222145 DOI: 10.1038/s41564-024-01707-9] [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: 07/28/2023] [Accepted: 04/19/2024] [Indexed: 05/30/2024]
Abstract
Nucleosomes are DNA-protein complexes composed of histone proteins that form the basis of eukaryotic chromatin. The nucleosome was a key innovation during eukaryotic evolution, but its origin from histone homologues in Archaea remains unclear. Viral histone repeats, consisting of multiple histone paralogues within a single protein, may reflect an intermediate state. Here we examine the diversity of histones encoded by Nucleocytoviricota viruses. We identified 258 histones from 168 viral metagenomes with variable domain configurations including histone singlets, doublets, triplets and quadruplets, the latter comprising the four core histones arranged in series. Viral histone repeats branch phylogenetically between Archaea and eukaryotes and display intermediate functions in Escherichia coli, self-assembling into eukaryotic-like nucleosomes that stack into archaeal-like oligomers capable of impacting genomic activity and condensing DNA. Histone linkage also facilitates nucleosome formation, promoting eukaryotic histone assembly in E. coli. These data support the hypothesis that viral histone repeats originated in stem-eukaryotes and that nucleosome evolution proceeded through histone repeat intermediates.
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Affiliation(s)
- Nicholas A T Irwin
- Merton College, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
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20
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Tang S, Huang CH, Ko TP, Lin KF, Chang YC, Lin PY, Sun L, Chen CY. Dual dimeric interactions in the nucleic acid-binding protein Sac10b lead to multiple bridging of double-stranded DNA. Heliyon 2024; 10:e31630. [PMID: 38867953 PMCID: PMC11167270 DOI: 10.1016/j.heliyon.2024.e31630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/26/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024] Open
Abstract
Nucleoid-associated proteins play a crucial role in the compaction and regulation of genetic material across organisms. The Sac10b family, also known as Alba, comprises widely distributed and highly conserved nucleoid-associated proteins found in archaea. Sac10b is identified as the first 10 kDa DNA-binding protein in the thermoacidophile Sulfolobus acidocaldarius. Here, we present the crystal structures of two homologous proteins, Sac10b1 and Sac10b2, as well as the Sac10b1 mutant F59A, determined at a resolution of 1.4-2.0 Å. Electron microscopic images reveal the DNA-bridging capabilities of both Sac10b1 and Sac10b2, albeit to varying extents. Analyses of crystal packing and electron microscopic results suggest that Sac10b1 facilitates cooperative DNA binding, forming extensive bridged filaments via the conserved R58 and F59 residues at the dimer-dimer interface. Substitutions at R58 or F59 of Sac10b1 attenuate end-to-end association, resulting in non-cooperative DNA binding, and formation of small, bridged DNA segments in a way similar to Sac10b2. Analytical ultracentrifuge and circular dichroism confirm the presence of thermostable, acid-tolerant dimers in both Sac10b1 and Sac10b2. These findings attest to the functional role of Sac10b in organizing and stabilizing chromosomal DNA through distinct bridging interactions, particularly under extreme growth conditions.
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Affiliation(s)
- Songqiang Tang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Chun-Hsiang Huang
- Protein Diffraction Group, Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Fu Lin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yuan-Chih Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Po-Yen Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Liuchang Sun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Chin-Yu Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
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21
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Hocher A, Warnecke T. Nucleosomes at the Dawn of Eukaryotes. Genome Biol Evol 2024; 16:evae029. [PMID: 38366053 PMCID: PMC10919886 DOI: 10.1093/gbe/evae029] [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: 11/27/2023] [Revised: 01/09/2024] [Accepted: 02/11/2024] [Indexed: 02/18/2024] Open
Abstract
Genome regulation in eukaryotes revolves around the nucleosome, the fundamental building block of eukaryotic chromatin. Its constituent parts, the four core histones (H3, H4, H2A, H2B), are universal to eukaryotes. Yet despite its exceptional conservation and central role in orchestrating transcription, repair, and other DNA-templated processes, the origins and early evolution of the nucleosome remain opaque. Histone-fold proteins are also found in archaea, but the nucleosome we know-a hetero-octameric complex composed of histones with long, disordered tails-is a hallmark of eukaryotes. What were the properties of the earliest nucleosomes? Did ancestral histones inevitably assemble into nucleosomes? When and why did the four core histones evolve? This review will look at the evolution of the eukaryotic nucleosome from the vantage point of archaea, focusing on the key evolutionary transitions required to build a modern nucleosome. We will highlight recent work on the closest archaeal relatives of eukaryotes, the Asgardarchaea, and discuss what their histones can and cannot tell us about the early evolution of eukaryotic chromatin. We will also discuss how viruses have become an unexpected source of information about the evolutionary path toward the nucleosome. Finally, we highlight the properties of early nucleosomes as an area where new tools and data promise tangible progress in the not-too-distant future.
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Affiliation(s)
- Antoine Hocher
- Medical Research Council Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Tobias Warnecke
- Medical Research Council Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Trinity College, University of Oxford, Oxford, UK
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22
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Wenck BR, Vickerman RL, Burkhart BW, Santangelo TJ. Archaeal histone-based chromatin structures regulate transcription elongation rates. Commun Biol 2024; 7:236. [PMID: 38413771 PMCID: PMC10899632 DOI: 10.1038/s42003-024-05928-w] [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: 08/16/2023] [Accepted: 02/16/2024] [Indexed: 02/29/2024] Open
Abstract
Many archaea encode and express histone proteins to compact their genomes. Archaeal and eukaryotic histones share a near-identical fold that permits DNA wrapping through select histone-DNA contacts to generate chromatin-structures that must be traversed by RNA polymerase (RNAP) to generate transcripts. As archaeal histones can spontaneously assemble with a single histone isoform, single-histone chromatin variants provide an idealized platform to detail the impacts of distinct histone-DNA contacts on transcription efficiencies and to detail the role of the conserved cleavage stimulatory factor, Transcription Factor S (TFS), in assisting RNAP through chromatin landscapes. We demonstrate that substitution of histone residues that modify histone-DNA contacts or the three-dimensional chromatin structure result in radically altered transcription elongation rates and pausing patterns. Chromatin-barriers slow and pause RNAP, providing regulatory potential. The modest impacts of TFS on elongation rates through chromatin landscapes is correlated with TFS-dispensability from the archaeon Thermococcus kodakarensis. Our results detail the importance of distinct chromatin structures for archaeal gene expression and provide a unique perspective on the evolution of, and regulatory strategies imposed by, eukaryotic chromatin.
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Affiliation(s)
- Breanna R Wenck
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Robert L Vickerman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
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23
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Brouwer TB, Kaczmarczyk A, Zarguit I, Pham C, Dame RT, van Noort J. Unravelling DNA Organization with Single-Molecule Force Spectroscopy Using Magnetic Tweezers. Methods Mol Biol 2024; 2819:535-572. [PMID: 39028523 DOI: 10.1007/978-1-0716-3930-6_25] [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
Genomes carry the genetic blueprint of all living organisms. Their organization requires strong condensation as well as carefully regulated accessibility to specific genes for proper functioning of their hosts. The study of the structure and dynamics of the proteins that organize the genome has benefited tremendously from the development of single-molecule force spectroscopy techniques that allow for real-time, nanometer accuracy measurements of the compaction of DNA and manipulation with pico-Newton scale forces. Magnetic tweezers, in particular, have the unique ability to complement such force spectroscopy with the control over the linking number of the DNA molecule, which plays an important role when DNA-organizing proteins form or release wraps, loops, and bends in DNA. Here, we describe all the necessary steps to prepare DNA substrates for magnetic tweezers experiments, assemble flow cells, tether DNA to a magnetic bead inside a flow cell, and manipulate and record the extension of such DNA tethers. Furthermore, we explain how mechanical parameters of nucleoprotein filaments can be extracted from the data.
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Affiliation(s)
- Thomas B Brouwer
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Artur Kaczmarczyk
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Ilias Zarguit
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Chi Pham
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - John van Noort
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands.
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24
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Takemata N. How Do Thermophiles Organize Their Genomes? Microbes Environ 2024; 39:ME23087. [PMID: 38839371 PMCID: PMC11946384 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] [Received: 10/26/2023] [Accepted: 03/19/2024] [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, Kyoto 615–8510, Japan
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25
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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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26
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Zhao H, Wu H, Guseman A, Abeykoon D, Camara CM, Dalal Y, Fushman D, Papoian GA. The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea. PLoS Comput Biol 2024; 20:e1011721. [PMID: 38181064 PMCID: PMC10796010 DOI: 10.1371/journal.pcbi.1011721] [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: 08/15/2023] [Revised: 01/18/2024] [Accepted: 11/28/2023] [Indexed: 01/07/2024] Open
Abstract
Histones compact and store DNA in both Eukarya and Archaea, forming heterodimers in Eukarya and homodimers in Archaea. Despite this, the folding mechanism of histones across species remains unclear. Our study addresses this gap by investigating 11 types of histone and histone-like proteins across humans, Drosophila, and Archaea through multiscale molecular dynamics (MD) simulations, complemented by NMR and circular dichroism experiments. We confirm and elaborate on the widely applied "folding upon binding" mechanism of histone dimeric proteins and report a new alternative conformation, namely, the inverted non-native dimer, which may be a thermodynamically metastable configuration. Protein sequence analysis indicated that the inverted conformation arises from the hidden ancestral head-tail sequence symmetry underlying all histone proteins, which is congruent with the previously proposed histone evolution hypotheses. Finally, to explore the potential formations of homodimers in Eukarya, we utilized MD-based AWSEM and AI-based AlphaFold-Multimer models to predict their structures and conducted extensive all-atom MD simulations to examine their respective structural stabilities. Our results suggest that eukaryotic histones may also form stable homodimers, whereas their disordered tails bring significant structural asymmetry and tip the balance towards the formation of commonly observed heterotypic dimers.
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Affiliation(s)
- Haiqing Zhao
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hao Wu
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
| | - Alex Guseman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Dulith Abeykoon
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Christina M. Camara
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David Fushman
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Garegin A. Papoian
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
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27
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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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28
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Marinov GK, Bagdatli ST, Wu T, He C, Kundaje A, Greenleaf WJ. The chromatin landscape of the euryarchaeon Haloferax volcanii. Genome Biol 2023; 24:253. [PMID: 37932847 PMCID: PMC10626798 DOI: 10.1186/s13059-023-03095-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/24/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations first made in their archaeal ancestors. One of the most notable such features is nucleosomal chromatin, although archaeal histones and chromatin differ significantly from those of eukaryotes, not all archaea possess histones and it is not clear if histones are a main packaging component for all that do. Despite increased interest in archaeal chromatin in recent years, its properties have been little studied using genomic tools. RESULTS Here, we adapt the ATAC-seq assay to archaea and use it to map the accessible landscape of the genome of the euryarchaeote Haloferax volcanii. We integrate the resulting datasets with genome-wide maps of active transcription and single-stranded DNA (ssDNA) and find that while H. volcanii promoters exist in a preferentially accessible state, unlike most eukaryotes, modulation of transcriptional activity is not associated with changes in promoter accessibility. Applying orthogonal single-molecule footprinting methods, we quantify the absolute levels of physical protection of H. volcanii and find that Haloferax chromatin is similarly or only slightly more accessible, in aggregate, than that of eukaryotes. We also evaluate the degree of coordination of transcription within archaeal operons and make the unexpected observation that some CRISPR arrays are associated with highly prevalent ssDNA structures. CONCLUSIONS Our results provide the first comprehensive maps of chromatin accessibility and active transcription in Haloferax across conditions and thus a foundation for future functional studies of archaeal chromatin.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
| | - S Tansu Bagdatli
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Tong Wu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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29
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Marinov GK, Doughty B, Kundaje A, Greenleaf WJ. The landscape of the histone-organized chromatin of Bdellovibrionota bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564843. [PMID: 37961278 PMCID: PMC10634947 DOI: 10.1101/2023.10.30.564843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Histone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, histone proteins have recently been identified in a few bacterial clades, most notably the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared to histones in archaea and eukaryotes. However, no functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription and three-dimensional genome organization in a member of Bdellovibrionota (a Bacteriovorax strain). We find that, similar to what is observed in some archaea and in eukaryotes with compact genomes such as yeast, Bacteriovorax chromatin is characterized by preferential accessibility around promoter regions. Similar to eukaryotes, chromatin accessibility in Bacteriovorax positively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that unlike in yeast, but similar to the state of mammalian and fly promoters, Bacteriovorax promoters exhibit very strong polymerase pausing. Finally, similar to that of other bacteria without histones, the Bacteriovorax genome exists in a three-dimensional (3D) configuration organized by the parABS system along the axis defined by replication origin and termination regions. These results provide a foundation for understanding the chromatin biology of the unique Bdellovibrionota bacteria and the functional diversity in chromatin organization across the tree of life.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Benjamin Doughty
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Arc Institute, Palo Alto, California, USA
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30
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Hocher A, Laursen SP, Radford P, Tyson J, Lambert C, Stevens KM, Montoya A, Shliaha PV, Picardeau M, Sockett RE, Luger K, Warnecke T. Histones with an unconventional DNA-binding mode in vitro are major chromatin constituents in the bacterium Bdellovibrio bacteriovorus. Nat Microbiol 2023; 8:2006-2019. [PMID: 37814071 PMCID: PMC10627809 DOI: 10.1038/s41564-023-01492-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/08/2023] [Indexed: 10/11/2023]
Abstract
Histone proteins bind DNA and organize the genomes of eukaryotes and most archaea, whereas bacteria rely on different nucleoid-associated proteins. Homology searches have detected putative histone-fold domains in a few bacteria, but whether these function like archaeal/eukaryotic histones is unknown. Here we report that histones are major chromatin components in the bacteria Bdellovibrio bacteriovorus and Leptospira interrogans. Patterns of sequence evolution suggest important roles for histones in additional bacterial clades. Crystal structures (<2.0 Å) of the B. bacteriovorus histone (Bd0055) dimer and the histone-DNA complex confirm conserved histone-fold topology but indicate a distinct DNA-binding mode. Unlike known histones in eukaryotes, archaea and viruses, Bd0055 binds DNA end-on, forming a sheath of dimers encasing straight DNA rather than wrapping DNA around their outer surface. Our results demonstrate that histones are present across the tree of life and highlight potential evolutionary innovation in how they associate with DNA.
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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.
| | - Shawn P Laursen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Paul Radford
- School of Life Sciences, Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Jess Tyson
- School of Life Sciences, Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Carey Lambert
- School of Life Sciences, Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Kathryn M Stevens
- Medical Research Council London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Alex Montoya
- Medical Research Council London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Pavel V Shliaha
- Medical Research Council London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Mathieu Picardeau
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Biology of Spirochetes Unit, Paris, France
| | - R Elizabeth Sockett
- School of Life Sciences, Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - 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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31
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Ofer S, Blombach F, Erkelens AM, Barker D, Soloviev Z, Schwab S, Smollett K, Matelska D, Fouqueau T, van der Vis N, Kent NA, Thalassinos K, Dame RT, Werner F. DNA-bridging by an archaeal histone variant via a unique tetramerisation interface. Commun Biol 2023; 6:968. [PMID: 37740023 PMCID: PMC10516927 DOI: 10.1038/s42003-023-05348-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
In eukaryotes, histone paralogues form obligate heterodimers such as H3/H4 and H2A/H2B that assemble into octameric nucleosome particles. Archaeal histones are dimeric and assemble on DNA into 'hypernucleosome' particles of varying sizes with each dimer wrapping 30 bp of DNA. These are composed of canonical and variant histone paralogues, but the function of these variants is poorly understood. Here, we characterise the structure and function of the histone paralogue MJ1647 from Methanocaldococcus jannaschii that has a unique C-terminal extension enabling homotetramerisation. The 1.9 Å X-ray structure of a dimeric MJ1647 species, structural modelling of the tetramer, and site-directed mutagenesis reveal that the C-terminal tetramerization module consists of two alpha helices in a handshake arrangement. Unlike canonical histones, MJ1647 tetramers can bridge two DNA molecules in vitro. Using single-molecule tethered particle motion and DNA binding assays, we show that MJ1647 tetramers bind ~60 bp DNA and compact DNA in a highly cooperative manner. We furthermore show that MJ1647 effectively competes with the transcription machinery to block access to the promoter in vitro. To the best of our knowledge, MJ1647 is the first histone shown to have DNA bridging properties, which has important implications for genome structure and gene expression in archaea.
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Affiliation(s)
- Sapir Ofer
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Fabian Blombach
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Amanda M Erkelens
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Declan Barker
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Zoja Soloviev
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Samuel Schwab
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Katherine Smollett
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Dorota Matelska
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Thomas Fouqueau
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Nico van der Vis
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Nicholas A Kent
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Konstantinos Thalassinos
- 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, Leiden, the Netherlands.
| | - Finn Werner
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.
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32
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Cezanne A, Hoogenberg B, Baum B. Probing archaeal cell biology: exploring the use of dyes in the imaging of Sulfolobus cells. Front Microbiol 2023; 14:1233032. [PMID: 37731920 PMCID: PMC10508906 DOI: 10.3389/fmicb.2023.1233032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/17/2023] [Indexed: 09/22/2023] Open
Abstract
Archaea are key players in many critical ecological processes. In comparison to eukaryotes and bacteria, however, our understanding of both the cell biology and diversity of archaea remains limited. While archaea inhabit a wide range of environmental conditions, many species are extremophiles, surviving in extreme temperature, salt or pH conditions, making their cell biology hard to study. Recently, our understanding of archaeal cell biology has been advanced significantly by the advent of live cell imaging in extremis as well as the development of genetic tools to exogenously express fluorescent proteins in some mesophilic archaeal model systems, e.g., Haloferax volcanii. However, for most archaeal species, especially thermophilic species or emerging model systems without well characterized genetic tools, live cell imaging remains dependent on fluorescent chemical probes to label and track the dynamics of living cells. While a wide range of fluorescent stains and markers that label different components of the cell are available commercially, their use has usually been optimized for use in a small number of eukaryotic cell systems. Here we report the successes and failures of the application of membrane, DNA, S-layer and cytoplasm markers in live cell imaging of archaea, as well as the optimization of fixation and immunolabelling approaches. We have applied these markers to the thermoacidophilic archaeon Sulfolobus acidocaldarius, but expect some to work in other archaeal species. Furthermore, those procedures that failed in S. acidocaldarius may still prove useful for imaging archaea that grow at a more neutral pH and/or at a less extreme temperature.
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Affiliation(s)
- Alice Cezanne
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Baukje Hoogenberg
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Buzz Baum
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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33
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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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34
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Deák G, Wapenaar H, Sandoval G, Chen R, Taylor MRD, Burdett H, Watson J, Tuijtel M, Webb S, Wilson M. Histone divergence in trypanosomes results in unique alterations to nucleosome structure. Nucleic Acids Res 2023; 51:7882-7899. [PMID: 37427792 PMCID: PMC10450195 DOI: 10.1093/nar/gkad577] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/02/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023] Open
Abstract
Eukaryotes have a multitude of diverse mechanisms for organising and using their genomes, but the histones that make up chromatin are highly conserved. Unusually, histones from kinetoplastids are highly divergent. The structural and functional consequences of this variation are unknown. Here, we have biochemically and structurally characterised nucleosome core particles (NCPs) from the kinetoplastid parasite Trypanosoma brucei. A structure of the T. brucei NCP reveals that global histone architecture is conserved, but specific sequence alterations lead to distinct DNA and protein interaction interfaces. The T. brucei NCP is unstable and has weakened overall DNA binding. However, dramatic changes at the H2A-H2B interface introduce local reinforcement of DNA contacts. The T. brucei acidic patch has altered topology and is refractory to known binders, indicating that the nature of chromatin interactions in T. brucei may be unique. Overall, our results provide a detailed molecular basis for understanding evolutionary divergence in chromatin structure.
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Affiliation(s)
- Gauri Deák
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Hannah Wapenaar
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Gorka Sandoval
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Ruofan Chen
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Mark R D Taylor
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Hayden Burdett
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - James A Watson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Maarten W Tuijtel
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Shaun Webb
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
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35
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Stevens KM, Warnecke T. Histone variants in archaea - An undiscovered country. Semin Cell Dev Biol 2023; 135:50-58. [PMID: 35221208 DOI: 10.1016/j.semcdb.2022.02.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/20/2022] [Accepted: 02/20/2022] [Indexed: 12/23/2022]
Abstract
Exchanging core histones in the nucleosome for paralogous variants can have important functional ramifications. Many of these variants, and their physiological roles, have been characterized in exquisite detail in model eukaryotes, including humans. In comparison, our knowledge of histone biology in archaea remains rudimentary. This is true in particular for our knowledge of histone variants. Many archaea encode several histone genes that differ in sequence, but do these paralogs make distinct, adaptive contributions to genome organization and regulation in a manner comparable to eukaryotes? Below, we review what we know about histone variants in archaea at the level of structure, regulation, and evolution. In all areas, our knowledge pales when compared to the wealth of insight that has been gathered for eukaryotes. Recent findings, however, provide tantalizing glimpses into a rich and largely undiscovered country that is at times familiar and eukaryote-like and at times strange and uniquely archaeal. We sketch a preliminary roadmap for further exploration of this country; an undertaking that may ultimately shed light not only on chromatin biology in archaea but also on the origin of histone-based chromatin in eukaryotes.
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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
| | - 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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36
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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: 0.5] [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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Lorch Y, Kornberg RD, Maier-Davis B. Role of the histone tails in histone octamer transfer. Nucleic Acids Res 2023; 51:3671-3678. [PMID: 36772826 PMCID: PMC10164550 DOI: 10.1093/nar/gkad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/17/2023] [Accepted: 01/25/2023] [Indexed: 02/12/2023] Open
Abstract
The exceptionally high positive charge of the histones, concentrated in the N- and C-terminal tails, is believed to contribute to the stability of the nucleosome by neutralizing the negative charge of the nucleosomal DNA. We find, on the contrary, that the high positive charge contributes to instability, performing an essential function in chromatin remodeling. We show that the tails are required for removal of the histone octamer by the RSC chromatin remodeling complex, and this function is not due to direct RSC-tail interaction. We also show that the tails are required for histone octamer transfer from nucleosomes to DNA, and this activity of the tails is a consequence of their positive charge. Thus, the histone tails, intrinsically disordered protein regions, perform a critical role in chromatin structure and transcription, unrelated to their well-known role in regulation through posttranscriptional modification.
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Affiliation(s)
- Yahli Lorch
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Barbara Maier-Davis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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38
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Erkelens AM, Henneman B, van der Valk RA, Kirolos NCS, Dame RT. Specific DNA binding of archaeal histones HMfA and HMfB. Front Microbiol 2023; 14:1166608. [PMID: 37143534 PMCID: PMC10151503 DOI: 10.3389/fmicb.2023.1166608] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
In archaea, histones play a role in genome compaction and are involved in transcription regulation. Whereas archaeal histones bind DNA without sequence specificity, they bind preferentially to DNA containing repeats of alternating A/T and G/C motifs. These motifs are also present on the artificial sequence "Clone20," a high-affinity model sequence for binding of the histones from Methanothermus fervidus. Here, we investigate the binding of HMfA and HMfB to Clone20 DNA. We show that specific binding at low protein concentrations (<30 nM) yields a modest level of DNA compaction, attributed to tetrameric nucleosome formation, whereas nonspecific binding strongly compacts DNA. We also demonstrate that histones impaired in hypernucleosome formation are still able to recognize the Clone20 sequence. Histone tetramers indeed exhibit a higher binding affinity for Clone20 than nonspecific DNA. Our results indicate that a high-affinity DNA sequence does not act as a nucleation site, but is bound by a tetramer which we propose is geometrically different from the hypernucleosome. Such a mode of histone binding might permit sequence-driven modulation of hypernucleosome size. These findings might be extrapolated to histone variants that do not form hypernucleosomes. Versatile binding modes of histones could provide a platform for functional interplay between genome compaction and transcription.
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Affiliation(s)
| | - Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | | | | | - Remus T. Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, Netherlands
- *Correspondence: Remus T. Dame,
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39
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Machida S, Diogo Dias J, Benkirane M. Faithful to the Marseille tradition: Unique and intriguing-that's how Marseillevirus packs its DNA. Mol Cell 2022; 82:4401-4402. [PMID: 36459981 DOI: 10.1016/j.molcel.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022]
Abstract
Not only does Marseillevirus bear the name of the city where it was identified, it also encompasses its values and what makes Marseille a wonderful city. Marseillevirus is unique and intriguing. As such, Bryson et al. in this issue of Molecular Cell reveal how virion-associated Marseillevirus DNA is packed with nucleosomes.
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Affiliation(s)
- Shinichi Machida
- Department of Structural Virology, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Joao Diogo Dias
- Institut de Génétique Humaine, Université de Montpellier, Laboratoire de Virologie Moléculaire CNRS-UMR9002, 34000 Montpellier, France
| | - Monsef Benkirane
- Institut de Génétique Humaine, Université de Montpellier, Laboratoire de Virologie Moléculaire CNRS-UMR9002, 34000 Montpellier, France.
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40
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A giant virus genome is densely packaged by stable nucleosomes within virions. Mol Cell 2022; 82:4458-4470.e5. [PMID: 36370708 DOI: 10.1016/j.molcel.2022.10.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/09/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022]
Abstract
The two doublet histones of Marseillevirus are distantly related to the four eukaryotic core histones and wrap 121 base pairs of DNA to form remarkably similar nucleosomes. By permeabilizing Marseillevirus virions and performing genome-wide nuclease digestion, chemical cleavage, and mass spectrometry assays, we find that the higher-order organization of Marseillevirus chromatin fundamentally differs from that of eukaryotes. Marseillevirus nucleosomes fully protect DNA within virions as closely abutted 121-bp DNA-wrapped cores without linker DNA or phasing along genes. Likewise, we observed that nucleosomes reconstituted onto multi-copy tandem repeats of a nucleosome-positioning sequence are tightly packed. Dense promiscuous packing of fully wrapped nucleosomes rather than "beads on a string" with genic punctuation represents a distinct mode of DNA packaging by histones. We suggest that doublet histones have evolved for viral genome protection and may resemble an early stage of histone differentiation leading to the eukaryotic octameric nucleosome.
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41
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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: 7] [Impact Index Per Article: 2.3] [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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42
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Mandemaker IK, Mattiroli F. A new chromatin flavor to cap chromosomes: Where structure, function, and evolution meet. Mol Cell 2022; 82:4199-4201. [PMID: 36400007 DOI: 10.1016/j.molcel.2022.10.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 11/19/2022]
Abstract
Soman, A., Wong, S.Y., et al. find that telomeric DNA assembles into a new high-order chromatin structure resembling a columnar stack of nucleosomes with dynamic properties. This raises new questions on telomere biology mechanisms and chromatin evolution.
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Affiliation(s)
- Imke K Mandemaker
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Francesca Mattiroli
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
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43
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Nozawa K, Takizawa Y, Pierrakeas L, Sogawa-Fujiwara C, Saikusa K, Akashi S, Luk E, Kurumizaka H. Cryo-electron microscopy structure of the H3-H4 octasome: A nucleosome-like particle without histones H2A and H2B. Proc Natl Acad Sci U S A 2022; 119:e2206542119. [PMID: 36322721 PMCID: PMC9659345 DOI: 10.1073/pnas.2206542119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 09/26/2022] [Indexed: 03/16/2023] Open
Abstract
The canonical nucleosome, which represents the major packaging unit of eukaryotic chromatin, has an octameric core composed of two histone H2A-H2B and H3-H4 dimers with ∼147 base pairs (bp) of DNA wrapped around it. Non-nucleosomal particles with alternative histone stoichiometries and DNA wrapping configurations have been found, and they could profoundly influence genome architecture and function. Using cryo-electron microscopy, we solved the structure of the H3-H4 octasome, a nucleosome-like particle with a di-tetrameric core consisting exclusively of the H3 and H4 histones. The core is wrapped by ∼120 bp of DNA in 1.5 negative superhelical turns, forming two stacked disks that are connected by a H4-H4' four-helix bundle. Three conformations corresponding to alternative interdisk angles were observed, indicating the flexibility of the H3-H4 octasome structure. In vivo crosslinking experiments detected histone-histone interactions consistent with the H3-H4 octasome model, suggesting that H3-H4 octasomes or related structural features exist in cells.
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Affiliation(s)
- Kayo Nozawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Leonidas Pierrakeas
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794
| | - Chizuru Sogawa-Fujiwara
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Kazumi Saikusa
- National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8563, Japan
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Ed Luk
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
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44
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How to Shut Down Transcription in Archaea during Virus Infection. Microorganisms 2022; 10:microorganisms10091824. [PMID: 36144426 PMCID: PMC9501531 DOI: 10.3390/microorganisms10091824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
Multisubunit RNA polymerases (RNAPs) carry out transcription in all domains of life; during virus infection, RNAPs are targeted by transcription factors encoded by either the cell or the virus, resulting in the global repression of transcription with distinct outcomes for different host–virus combinations. These repressors serve as versatile molecular probes to study RNAP mechanisms, as well as aid the exploration of druggable sites for the development of new antibiotics. Here, we review the mechanisms and structural basis of RNAP inhibition by the viral repressor RIP and the crenarchaeal negative regulator TFS4, which follow distinct strategies. RIP operates by occluding the DNA-binding channel and mimicking the initiation factor TFB/TFIIB. RIP binds tightly to the clamp and locks it into one fixed position, thereby preventing conformational oscillations that are critical for RNAP function as it progresses through the transcription cycle. TFS4 engages with RNAP in a similar manner to transcript cleavage factors such as TFS/TFIIS through the NTP-entry channel; TFS4 interferes with the trigger loop and bridge helix within the active site by occlusion and allosteric mechanisms, respectively. The conformational changes in RNAP described above are universally conserved and are also seen in inactive dimers of eukaryotic RNAPI and several inhibited RNAP complexes of both bacterial and eukaryotic RNA polymerases, including inactive states that precede transcription termination. A comparison of target sites and inhibitory mechanisms reveals that proteinaceous repressors and RNAP-specific antibiotics use surprisingly common ways to inhibit RNAP function.
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45
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Columnar structure of human telomeric chromatin. Nature 2022; 609:1048-1055. [PMID: 36104563 DOI: 10.1038/s41586-022-05236-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 08/12/2022] [Indexed: 01/11/2023]
Abstract
Telomeres, the ends of eukaryotic chromosomes, play pivotal parts in ageing and cancer and are targets of DNA damage and the DNA damage response1-5. Little is known about the structure of telomeric chromatin at the molecular level. Here we used negative stain electron microscopy and single-molecule magnetic tweezers to characterize 3-kbp-long telomeric chromatin fibres. We also obtained the cryogenic electron microscopy structure of the condensed telomeric tetranucleosome and its dinucleosome unit. The structure displayed close stacking of nucleosomes with a columnar arrangement, and an unusually short nucleosome repeat length that comprised about 132 bp DNA wound in a continuous superhelix around histone octamers. This columnar structure is primarily stabilized by the H2A carboxy-terminal and histone amino-terminal tails in a synergistic manner. The columnar conformation results in exposure of the DNA helix, which may make it susceptible to both DNA damage and the DNA damage response. The conformation also exists in an alternative open state, in which one nucleosome is unstacked and flipped out, which exposes the acidic patch of the histone surface. The structural features revealed in this work suggest mechanisms by which protein factors involved in telomere maintenance can access telomeric chromatin in its compact form.
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46
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Profile of Karolin Luger. Proc Natl Acad Sci U S A 2022; 119:e2212317119. [PMID: 35939715 PMCID: PMC9407286 DOI: 10.1073/pnas.2212317119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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47
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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: 0.3] [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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48
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Song A, Chen FX. The pleiotropic roles of SPT5 in transcription. Transcription 2022; 13:53-69. [PMID: 35876486 PMCID: PMC9467590 DOI: 10.1080/21541264.2022.2103366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Initially discovered by genetic screens in budding yeast, SPT5 and its partner SPT4 form a stable complex known as DSIF in metazoa, which plays pleiotropic roles in multiple steps of transcription. SPT5 is the most conserved transcription elongation factor, being found in all three domains of life; however, its structure has evolved to include new domains and associated posttranslational modifications. These gained features have expanded transcriptional functions of SPT5, likely to meet the demand for increasingly complex regulation of transcription in higher organisms. This review discusses the pleiotropic roles of SPT5 in transcription, including RNA polymerase II (Pol II) stabilization, enhancer activation, Pol II pausing and its release, elongation, and termination, with a focus on the most recent progress of SPT5 functions in regulating metazoan transcription.
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Affiliation(s)
- Aixia Song
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, Province 200032, China
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, Province 200032, China
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49
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Grau-Bové X, Navarrete C, Chiva C, Pribasnig T, Antó M, Torruella G, Galindo LJ, Lang BF, Moreira D, López-Garcia P, Ruiz-Trillo I, Schleper C, Sabidó E, Sebé-Pedrós A. A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. Nat Ecol Evol 2022; 6:1007-1023. [PMID: 35680998 PMCID: PMC7613034 DOI: 10.1038/s41559-022-01771-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/21/2022] [Indexed: 02/06/2023]
Abstract
Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically-comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in Archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (e.g., methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.
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Affiliation(s)
- Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Navarrete
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Thomas Pribasnig
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Meritxell Antó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Guifré Torruella
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Luis Javier Galindo
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Bernd Franz Lang
- Robert Cedergren Centre in Bioinformatics and Genomics, Department of Biochemistry, Université de Montréal, Montréal, Quebec, Canada
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-Garcia
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius. Biomolecules 2022; 12:biom12040524. [PMID: 35454113 PMCID: PMC9025068 DOI: 10.3390/biom12040524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 02/06/2023] Open
Abstract
In archaeal microorganisms, the compaction and organization of the chromosome into a dynamic but condensed structure is mediated by diverse chromatin-organizing proteins in a lineage-specific manner. While many archaea employ eukaryotic-type histones for nucleoid organization, this is not the case for the crenarchaeal model species Sulfolobus acidocaldarius and related species in Sulfolobales, in which the organization appears to be mostly reliant on the action of small basic DNA-binding proteins. There is still a lack of a full understanding of the involved proteins and their functioning. Here, a combination of in vitro and in vivo methodologies is used to study the DNA-binding properties of Sul12a, an uncharacterized small basic protein conserved in several Sulfolobales species displaying a winged helix–turn–helix structural motif and annotated as a transcription factor. Genome-wide chromatin immunoprecipitation and target-specific electrophoretic mobility shift assays demonstrate that Sul12a of S. acidocaldarius interacts with DNA in a non-sequence specific manner, while atomic force microscopy imaging of Sul12a–DNA complexes indicate that the protein induces structural effects on the DNA template. Based on these results, and a contrario to its initial annotation, it can be concluded that Sul12a is a novel chromatin-organizing protein.
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