1
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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] [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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2
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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: 0] [Impact Index Per Article: 0] [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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3
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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: 0] [Impact Index Per Article: 0] [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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4
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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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5
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Sakrikar S, Schmid A. An archaeal histone-like protein regulates gene expression in response to salt stress. Nucleic Acids Res 2021; 49:12732-12743. [PMID: 34883507 PMCID: PMC8682779 DOI: 10.1093/nar/gkab1175] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 12/21/2022] Open
Abstract
Histones, ubiquitous in eukaryotes as DNA-packing proteins, find their evolutionary origins in archaea. Unlike the characterized histone proteins of a number of methanogenic and themophilic archaea, previous research indicated that HpyA, the sole histone encoded in the model halophile Halobacterium salinarum, is not involved in DNA packaging. Instead, it was found to have widespread but subtle effects on gene expression and to maintain wild type cell morphology. However, the precise function of halophilic histone-like proteins remain unclear. Here we use quantitative phenotyping, genetics, and functional genomics to investigate HpyA function. These experiments revealed that HpyA is important for growth and rod-shaped morphology in reduced salinity. HpyA preferentially binds DNA at discrete genomic sites under low salt to regulate expression of ion uptake, particularly iron. HpyA also globally but indirectly activates other ion uptake and nucleotide biosynthesis pathways in a salt-dependent manner. Taken together, these results demonstrate an alternative function for an archaeal histone-like protein as a transcriptional regulator, with its function tuned to the physiological stressors of the hypersaline environment.
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Affiliation(s)
- Saaz Sakrikar
- Biology Department, Duke University, Durham, NC27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC27708, USA
| | - Amy K Schmid
- Biology Department, Duke University, Durham, NC27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC27708, USA
- Center for Genomics and Computational Biology, Duke University, Durham, NC27708, USA
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6
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Villain P, da Cunha V, Villain E, Forterre P, Oberto J, Catchpole R, Basta T. The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase. Nucleic Acids Res 2021; 49:12332-12347. [PMID: 34755863 PMCID: PMC8643681 DOI: 10.1093/nar/gkab869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/10/2021] [Accepted: 11/02/2021] [Indexed: 01/15/2023] Open
Abstract
In all cells, DNA topoisomerases dynamically regulate DNA supercoiling allowing essential DNA processes such as transcription and replication to occur. How this complex system emerged in the course of evolution is poorly understood. Intriguingly, a single horizontal gene transfer event led to the successful establishment of bacterial gyrase in Archaea, but its emergent function remains a mystery. To better understand the challenges associated with the establishment of pervasive negative supercoiling activity, we expressed the gyrase of the bacterium Thermotoga maritima in a naïve archaeon Thermococcus kodakarensis which naturally has positively supercoiled DNA. We found that the gyrase was catalytically active in T. kodakarensis leading to strong negative supercoiling of plasmid DNA which was stably maintained over at least eighty generations. An increased sensitivity of gyrase-expressing T. kodakarensis to ciprofloxacin suggested that gyrase also modulated chromosomal topology. Accordingly, global transcriptome analyses revealed large scale gene expression deregulation and identified a subset of genes responding to the negative supercoiling activity of gyrase. Surprisingly, the artificially introduced dominant negative supercoiling activity did not have a measurable effect on T. kodakarensis growth rate. Our data suggest that gyrase can become established in Thermococcales archaea without critically interfering with DNA transaction processes.
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Affiliation(s)
- Paul Villain
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Violette da Cunha
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | - Patrick Forterre
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.,Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Jacques Oberto
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Ryan Catchpole
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Tamara Basta
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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7
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Bowerman S, Wereszczynski J, Luger K. Archaeal chromatin 'slinkies' are inherently dynamic complexes with deflected DNA wrapping pathways. eLife 2021; 10:65587. [PMID: 33650488 PMCID: PMC7990501 DOI: 10.7554/elife.65587] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
Eukaryotes and many archaea package their DNA with histones. While the four eukaryotic histones wrap ~147 DNA base pairs into nucleosomes, archaeal histones form ‘nucleosome-like’ complexes that continuously wind between 60 and 500 base pairs of DNA (‘archaeasomes’), suggested by crystal contacts and analysis of cellular chromatin. Solution structures of large archaeasomes (>90 DNA base pairs) have never been directly observed. Here, we utilize molecular dynamics simulations, analytical ultracentrifugation, and cryoEM to structurally characterize the solution state of archaeasomes on longer DNA. Simulations reveal dynamics of increased accessibility without disruption of DNA-binding or tetramerization interfaces. Mg2+ concentration influences compaction, and cryoEM densities illustrate that DNA is wrapped in consecutive substates arranged 90o out-of-plane with one another. Without ATP-dependent remodelers, archaea may leverage these inherent dynamics to balance chromatin packing and accessibility. All animals, plants and fungi belong to a group of living organisms called eukaryotes. The two other groups are bacteria and archaea, which include unicellular, microscopic organisms. All three groups have genes, which are typically stored on long strands of DNA. Eukaryotes have so much DNA that they use proteins called histones to help package and organize it inside each cell. Archaea also have simplified histones that help store their DNA, and studying these proteins could reveal how eukaryotic histones first evolved. In eukaryotes, groups of eight histones form a short cylinder that organizes a small section of DNA into a structure called a nucleosome. Each cell needs hundreds of thousands of nucleosomes to arrange its DNA. Eukaryotic cells also contain other proteins that release pieces of DNA from histones so that their genetic information can be used. The histones in Archaea don’t form discrete nucleosomes, instead, they coil DNA into ‘slinky-like’ shapes. It’s still unclear how DNA packing in archaea works and how it differs from eukaryotes. Bowerman, Wereszczynski and Luger used computer simulations, biochemistry and cryo-electron microscopy to study the histones from archaea. The archaeal ‘slinky-like’ histone structures are more flexible than nucleosomes, and can open and close like clamshells. This flexibility allows the information in the genomes of Archaea to be easily accessed, so, unlike in eukaryotes, archaeal cells may not need other proteins to release the DNA from the histones. The ability to package DNA allows cells to contain many more genes, so evolving histones was a vital step in the evolution of eukaryotic life, including the appearance of animals. Archaeal histones may reflect early versions of histones in eukaryotes, and can be used to understand how DNA packing has evolved. Furthermore, a greater understanding of Archaea may help better explain their role in health and global ecosystems, and allow their use in industrial applications.
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Affiliation(s)
- Samuel Bowerman
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, United States
| | - Jeff Wereszczynski
- Department of Physics and Center for the Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, United States
| | - Karolin Luger
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, United States
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8
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Hocher A, Rojec M, Swadling JB, Esin A, Warnecke T. The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog. eLife 2019; 8:52542. [PMID: 31710291 PMCID: PMC6877293 DOI: 10.7554/elife.52542] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/10/2019] [Indexed: 02/06/2023] Open
Abstract
Histones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are widespread but not universal: several lineages have lost histone genes. What prompted or facilitated these losses and how archaea without histones organize their chromatin remains largely unknown. Here, we elucidate primary chromatin architecture in an archaeon without histones, Thermoplasma acidophilum, which harbors a HU family protein (HTa) that protects part of the genome from micrococcal nuclease digestion. Charting HTa-based chromatin architecture in vitro, in vivo and in an HTa-expressing E. coli strain, we present evidence that HTa is an archaeal histone analog. HTa preferentially binds to GC-rich sequences, exhibits invariant positioning throughout the growth cycle, and shows archaeal histone-like oligomerization behavior. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.
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Affiliation(s)
- Antoine Hocher
- MRC London Institute of Medical Sciences (LMS), London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College, London, United Kingdom
| | - Maria Rojec
- MRC London Institute of Medical Sciences (LMS), London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College, London, United Kingdom
| | - Jacob B Swadling
- MRC London Institute of Medical Sciences (LMS), London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College, London, United Kingdom
| | - Alexander Esin
- MRC London Institute of Medical Sciences (LMS), London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College, London, United Kingdom
| | - Tobias Warnecke
- MRC London Institute of Medical Sciences (LMS), London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College, London, United Kingdom
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9
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Rojec M, Hocher A, Stevens KM, Merkenschlager M, Warnecke T. Chromatinization of Escherichia coli with archaeal histones. eLife 2019; 8:49038. [PMID: 31692448 PMCID: PMC6867714 DOI: 10.7554/elife.49038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/05/2019] [Indexed: 12/12/2022] Open
Abstract
Nucleosomes restrict DNA accessibility throughout eukaryotic genomes, with repercussions for replication, transcription, and other DNA-templated processes. How this globally restrictive organization emerged during evolution remains poorly understood. Here, to better understand the challenges associated with establishing globally restrictive chromatin, we express histones in a naive system that has not evolved to deal with nucleosomal structures: Escherichia coli. We find that histone proteins from the archaeon Methanothermus fervidus assemble on the E. coli chromosome in vivo and protect DNA from micrococcal nuclease digestion, allowing us to map binding footprints genome-wide. We show that higher nucleosome occupancy at promoters is associated with lower transcript levels, consistent with local repressive effects. Surprisingly, however, this sudden enforced chromatinization has only mild repercussions for growth unless cells experience topological stress. Our results suggest that histones can become established as ubiquitous chromatin proteins without interfering critically with key DNA-templated processes.
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Affiliation(s)
- Maria Rojec
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Antoine Hocher
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - 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
| | - Matthias Merkenschlager
- 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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10
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Sanders TJ, Marshall CJ, Santangelo TJ. The Role of Archaeal Chromatin in Transcription. J Mol Biol 2019; 431:4103-4115. [PMID: 31082442 PMCID: PMC6842674 DOI: 10.1016/j.jmb.2019.05.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/02/2019] [Accepted: 05/04/2019] [Indexed: 02/08/2023]
Abstract
Genomic organization impacts accessibility and movement of information processing systems along DNA. DNA-bound proteins dynamically dictate gene expression and provide regulatory potential to tune transcription rates to match ever-changing environmental conditions. Archaeal genomes are typically small, circular, gene dense, and organized either by histone proteins that are homologous to their eukaryotic counterparts, or small basic proteins that function analogously to bacterial nucleoid proteins. We review here how archaeal genomes are organized and how such organization impacts archaeal gene expression, focusing on conserved DNA-binding proteins within the clade and the factors that are known to impact transcription initiation and elongation within protein-bound genomes.
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Affiliation(s)
- Travis J Sanders
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Craig J Marshall
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
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11
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Talbert PB, Meers MP, Henikoff S. Old cogs, new tricks: the evolution of gene expression in a chromatin context. Nat Rev Genet 2019; 20:283-297. [PMID: 30886348 DOI: 10.1038/s41576-019-0105-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sophisticated gene-regulatory mechanisms probably evolved in prokaryotes billions of years before the emergence of modern eukaryotes, which inherited the same basic enzymatic machineries. However, the epigenomic landscapes of eukaryotes are dominated by nucleosomes, which have acquired roles in genome packaging, mitotic condensation and silencing parasitic genomic elements. Although the molecular mechanisms by which nucleosomes are displaced and modified have been described, just how transcription factors, histone variants and modifications and chromatin regulators act on nucleosomes to regulate transcription is the subject of considerable ongoing study. We explore the extent to which these transcriptional regulatory components function in the context of the evolutionarily ancient role of chromatin as a barrier to processes acting on DNA and how chromatin proteins have diversified to carry out evolutionarily recent functions that accompanied the emergence of differentiation and development in multicellular eukaryotes.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael P Meers
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
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12
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Sanders TJ, Lammers M, Marshall CJ, Walker JE, Lynch ER, Santangelo TJ. TFS and Spt4/5 accelerate transcription through archaeal histone-based chromatin. Mol Microbiol 2019; 111:784-797. [PMID: 30592095 PMCID: PMC6417941 DOI: 10.1111/mmi.14191] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2018] [Indexed: 12/25/2022]
Abstract
RNA polymerase must surmount translocation barriers for continued transcription. In Eukarya and most Archaea, DNA-bound histone proteins represent the most common and troublesome barrier to transcription elongation. Eukaryotes encode a plethora of chromatin-remodeling complexes, histone-modification enzymes and transcription elongation factors to aid transcription through nucleosomes, while archaea seemingly lack machinery to remodel/modify histone-based chromatin and thus must rely on elongation factors to accelerate transcription through chromatin-barriers. TFS (TFIIS in Eukarya) and the Spt4-Spt5 complex are universally encoded in archaeal genomes, and here we demonstrate that both elongation factors, via different mechanisms, can accelerate transcription through archaeal histone-based chromatin. Histone proteins in Thermococcus kodakarensis are sufficiently abundant to completely wrap all genomic DNA, resulting in a consistent protein barrier to transcription elongation. TFS-enhanced cleavage of RNAs in backtracked transcription complexes reactivates stalled RNAPs and dramatically accelerates transcription through histone-barriers, while Spt4-Spt5 changes to clamp-domain dynamics play a lesser-role in stabilizing transcription. Repeated attempts to delete TFS, Spt4 and Spt5 from the T. kodakarensis genome were not successful, and the essentiality of both conserved transcription elongation factors suggests that both conserved elongation factors play important roles in transcription regulation in vivo, including mechanisms to accelerate transcription through downstream protein barriers.
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Affiliation(s)
- Travis J. Sanders
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Marshall Lammers
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Craig J. Marshall
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Julie E. Walker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
- Current address: Renewable and Sustainable Energy Institute, University of Colorado, Boulder, Colorado, 80303, USA
| | - Erin R. Lynch
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Thomas J. Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
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13
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Abstract
The genomes of all organisms throughout the tree of life are compacted and organized in chromatin by association of chromatin proteins. Eukaryotic genomes encode histones, which are assembled on the genome into octamers, yielding nucleosomes. Post-translational modifications of the histones, which occur mostly on their N-terminal tails, define the functional state of chromatin. Like eukaryotes, most archaeal genomes encode histones, which are believed to be involved in the compaction and organization of their genomes. Instead of discrete multimers, in vivo data suggest assembly of “nucleosomes” of variable size, consisting of multiples of dimers, which are able to induce repression of transcription. Based on these data and a model derived from X-ray crystallography, it was recently proposed that archaeal histones assemble on DNA into “endless” hypernucleosomes. In this review, we discuss the amino acid determinants of hypernucleosome formation and highlight differences with the canonical eukaryotic octamer. We identify archaeal histones differing from the consensus, which are expected to be unable to assemble into hypernucleosomes. Finally, we identify atypical archaeal histones with short N- or C-terminal extensions and C-terminal tails similar to the tails of eukaryotic histones, which are subject to post-translational modification. Based on the expected characteristics of these archaeal histones, we discuss possibilities of involvement of histones in archaeal transcription regulation. Both Archaea and eukaryotes express histones, but whereas the tertiary structure of histones is conserved, the quaternary structure of histone–DNA complexes is very different. In a recent study, the crystal structure of the archaeal hypernucleosome was revealed to be an “endless” core of interacting histones that wraps the DNA around it in a left-handed manner. The ability to form a hypernucleosome is likely determined by dimer–dimer interactions as well as stacking interactions between individual layers of the hypernucleosome. We analyzed a wide variety of archaeal histones and found that most but not all histones possess residues able to facilitate hypernucleosome formation. Among these are histones with truncated termini or extended histone tails. Based on our analysis, we propose several possibilities of archaeal histone involvement in transcription regulation.
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Affiliation(s)
- Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Clara van Emmerik
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Hugo van Ingen
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Remus T. Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
- * E-mail:
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14
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Azad GK, Swagatika S, Kumawat M, Kumawat R, Tomar RS. Modifying Chromatin by Histone Tail Clipping. J Mol Biol 2018; 430:3051-3067. [DOI: 10.1016/j.jmb.2018.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 12/15/2022]
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15
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Abstract
Transcription elongation is not uniform and transcription is often hindered by protein-bound factors or DNA lesions that limit translocation and impair catalysis. Despite the high degree of sequence and structural homology of the multi-subunit RNA polymerases (RNAP), substantial differences in response to DNA lesions have been reported. Archaea encode only a single RNAP with striking structural conservation with eukaryotic RNAP II (Pol II). Here, we demonstrate that the archaeal RNAP from Thermococcus kodakarensis is sensitive to a variety of DNA lesions that pause and arrest RNAP at or adjacent to the site of DNA damage. DNA damage only halts elongation when present in the template strand, and the damage often results in RNAP arresting such that the lesion would be encapsulated with the transcription elongation complex. The strand-specific halt to archaeal transcription elongation on modified templates is supportive of RNAP recognizing DNA damage and potentially initiating DNA repair through a process akin to the well-described transcription-coupled DNA repair (TCR) pathways in Bacteria and Eukarya.
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Affiliation(s)
- Alexandra M Gehring
- a Department of Biochemistry and Molecular Biology , Colorado State University , Fort Collins , CO , USA.,b Institute for Genome Architecture and Function, Colorado State University , Fort Collins , CO , USA
| | - Thomas J Santangelo
- a Department of Biochemistry and Molecular Biology , Colorado State University , Fort Collins , CO , USA.,b Institute for Genome Architecture and Function, Colorado State University , Fort Collins , CO , USA
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16
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Nishida H, Oshima T. Archaeal histone distribution is associated with archaeal genome base composition. J GEN APPL MICROBIOL 2016; 63:28-35. [PMID: 27990001 DOI: 10.2323/jgam.2016.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A subpopulation of Archaea possesses histones, which are similar to eukaryotic histones H3 and H4. However, archaeal histones are smaller than H3 and H4, and are not post-translationally modified. In addition, the fundamental unit of archaeal histones might be a dimer. The organization of archaeal nucleosomes, therefore, differs from that of eukaryotic nucleosomes. The base compositions of archaeal genome are much more diversified than those of eukaryote and the archaeal histones have more diversified amino acid sequences, which are reflected by their varied isoelectric points. We hypothesized that the highly diversified archaeal genomic DNA base composition may cause the archaeal histone variation. Phylogenetic analysis revealed that the distribution of archaeal histones is associated with their genomic DNA base composition. This result strongly suggests that archaeal histones have evolved concomitantly with their genomic DNA base composition. Eukaryotic histones are one of the most evolutionarily conserved proteins and would limit the diversification of genomic DNA base composition. In contrast, archaeal histones have diversified and would permit the great diversification of genomic DNA base composition.
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Affiliation(s)
- Hiromi Nishida
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University
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17
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Abstract
The known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. Accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. Archaea are reliant on a single RNA polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcription mimic strategies also employed for eukaryotic and bacterial species. Novel mechanisms of transcription regulation have become apparent by increasingly sophisticated in vivo and in vitro investigations of archaeal species. This review emphasizes recent progress in understanding archaeal transcription regulatory mechanisms and highlights insights gained from studies of the influence of archaeal chromatin on transcription.
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Audin MJC, Wurm JP, Cvetkovic MA, Sprangers R. The oligomeric architecture of the archaeal exosome is important for processive and efficient RNA degradation. Nucleic Acids Res 2016; 44:2962-73. [PMID: 26837575 PMCID: PMC4824110 DOI: 10.1093/nar/gkw062] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/25/2016] [Indexed: 11/30/2022] Open
Abstract
The exosome plays an important role in RNA degradation and processing. In archaea, three Rrp41:Rrp42 heterodimers assemble into a barrel like structure that contains a narrow RNA entrance pore and a lumen that contains three active sites. Here, we demonstrate that this quaternary structure of the exosome is important for efficient RNA degradation. We find that the entrance pore of the barrel is required for nM substrate affinity. This strong interaction is crucial for processive substrate degradation and prevents premature release of the RNA from the enzyme. Using methyl TROSY NMR techniques, we establish that the 3′ end of the substrate remains highly flexible inside the lumen. As a result, the RNA jumps between the three active sites that all equally participate in substrate degradation. The RNA jumping rate is, however, much faster than the cleavage rate, indicating that not all active site:substrate encounters result in catalysis. Enzymatic turnover therefore benefits from the confinement of the active sites and substrate in the lumen, which ensures that the RNA is at all times bound to one of the active sites. The evolution of the exosome into a hexameric complex and the optimization of its catalytic efficiency were thus likely co-occurring events.
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Affiliation(s)
- Maxime J C Audin
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Jan Philip Wurm
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Milos A Cvetkovic
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Remco Sprangers
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
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19
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How Likely Are We? Evolution of Organismal Complexity. Evol Biol 2016. [DOI: 10.1007/978-3-319-41324-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Mechanisms of Evolutionary Innovation Point to Genetic Control Logic as the Key Difference Between Prokaryotes and Eukaryotes. J Mol Evol 2015. [PMID: 26208881 DOI: 10.1007/s00239-015-9688-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The evolution of life from the simplest, original form to complex, intelligent animal life occurred through a number of key innovations. Here we present a new tool to analyze these key innovations by proposing that the process of evolutionary innovation may follow one of three underlying processes, namely a Random Walk, a Critical Path, or a Many Paths process, and in some instances may also constitute a "Pull-up the Ladder" event. Our analysis is based on the occurrence of function in modern biology, rather than specific structure or mechanism. A function in modern biology may be classified in this way either on the basis of its evolution or the basis of its modern mechanism. Characterizing key innovations in this way helps identify the likelihood that an innovation could arise. In this paper, we describe the classification, and methods to classify functional features of modern organisms into these three classes based on the analysis of how a function is implemented in modern biology. We present the application of our categorization to the evolution of eukaryotic gene control. We use this approach to support the argument that there are few, and possibly no basic chemical differences between the functional constituents of the machinery of gene control between eukaryotes, bacteria and archaea. This suggests that the difference between eukaryotes and prokaryotes that allows the former to develop the complex genetic architecture seen in animals and plants is something other than their chemistry. We tentatively identify the difference as a difference in control logic, that prokaryotic genes are by default 'on' and eukaryotic genes are by default 'off.' The Many Paths evolutionary process suggests that, from a 'default off' starting point, the evolution of the genetic complexity of higher eukaryotes is a high probability event.
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21
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Peeters E, Driessen RPC, Werner F, Dame RT. The interplay between nucleoid organization and transcription in archaeal genomes. Nat Rev Microbiol 2015; 13:333-41. [PMID: 25944489 DOI: 10.1038/nrmicro3467] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The archaeal genome is organized by either eukaryotic-like histone proteins or bacterial-like nucleoid-associated proteins. Recent studies have revealed novel insights into chromatin dynamics and their effect on gene expression in archaeal model organisms. In this Progress article, we discuss the interplay between chromatin proteins, such as histones and Alba, and components of the basal transcription machinery, as well as between chromatin structure and gene-specific transcription factors in archaea. Such an interplay suggests that chromatin might have a role in regulating gene expression on both a global and a gene-specific level. Moreover, several archaeal transcription factors combine a global gene regulatory role with an architectural role, thus contributing to chromatin organization and compaction, as well as gene expression. We describe the emerging principles underlying how these factors cooperate in nucleoid structuring and gene regulation.
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Affiliation(s)
- Eveline Peeters
- 1] Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium. [2]
| | - Rosalie P C Driessen
- 1] Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands. [2]
| | - Finn Werner
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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22
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Chromatin structure and dynamics in hot environments: architectural proteins and DNA topoisomerases of thermophilic archaea. Int J Mol Sci 2014; 15:17162-87. [PMID: 25257534 PMCID: PMC4200833 DOI: 10.3390/ijms150917162] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/19/2014] [Accepted: 09/09/2014] [Indexed: 01/20/2023] Open
Abstract
In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.
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24
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Isom CE, Turner JL, Lessner DJ, Karr EA. Redox-sensitive DNA binding by homodimeric Methanosarcina acetivorans MsvR is modulated by cysteine residues. BMC Microbiol 2013; 13:163. [PMID: 23865844 PMCID: PMC3729527 DOI: 10.1186/1471-2180-13-163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 07/12/2013] [Indexed: 11/16/2022] Open
Abstract
Background Methanoarchaea are among the strictest known anaerobes, yet they can survive exposure to oxygen. The mechanisms by which they sense and respond to oxidizing conditions are unknown. MsvR is a transcription regulatory protein unique to the methanoarchaea. Initially identified and characterized in the methanogen Methanothermobacter thermautotrophicus (Mth), MthMsvR displays differential DNA binding under either oxidizing or reducing conditions. Since MthMsvR regulates a potential oxidative stress operon in M. thermautotrophicus, it was hypothesized that the MsvR family of proteins were redox-sensitive transcription regulators. Results An MsvR homologue from the methanogen Methanosarcina acetivorans, MaMsvR, was overexpressed and purified. The two MsvR proteins bound the same DNA sequence motif found upstream of all known MsvR encoding genes, but unlike MthMsvR, MaMsvR did not bind the promoters of select genes involved in the oxidative stress response. Unlike MthMsvR that bound DNA under both non-reducing and reducing conditions, MaMsvR bound DNA only under reducing conditions. MaMsvR appeared as a dimer in gel filtration chromatography analysis and site-directed mutagenesis suggested that conserved cysteine residues within the V4R domain were involved in conformational rearrangements that impact DNA binding. Conclusions Results presented herein suggest that homodimeric MaMsvR acts as a transcriptional repressor by binding Ma PmsvR under non-reducing conditions. Changing redox conditions promote conformational changes that abrogate binding to Ma PmsvR which likely leads to de-repression.
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Affiliation(s)
- Catherine E Isom
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
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25
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Nalabothula N, Xi L, Bhattacharyya S, Widom J, Wang JP, Reeve JN, Santangelo TJ, Fondufe-Mittendorf YN. Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs. BMC Genomics 2013; 14:391. [PMID: 23758892 PMCID: PMC3691661 DOI: 10.1186/1471-2164-14-391] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 05/31/2013] [Indexed: 02/03/2023] Open
Abstract
Background Histone wrapping of DNA into nucleosomes almost certainly evolved in the Archaea, and predates Eukaryotes. In Eukaryotes, nucleosome positioning plays a central role in regulating gene expression and is directed by primary sequence motifs that together form a nucleosome positioning code. The experiments reported were undertaken to determine if archaeal histone assembly conforms to the nucleosome positioning code. Results Eukaryotic nucleosome positioning is favored and directed by phased helical repeats of AA/TT/AT/TA and CC/GG/CG/GC dinucleotides, and disfavored by longer AT-rich oligonucleotides. Deep sequencing of genomic DNA protected from micrococcal nuclease digestion by assembly into archaeal nucleosomes has established that archaeal nucleosome assembly is also directed and positioned by these sequence motifs, both in vivo in Methanothermobacter thermautotrophicus and Thermococcus kodakarensis and in vitro in reaction mixtures containing only one purified archaeal histone and genomic DNA. Archaeal nucleosomes assembled at the same locations in vivo and in vitro, with much reduced assembly immediately upstream of open reading frames and throughout the ribosomal rDNA operons. Providing further support for a common positioning code, archaeal histones assembled into nucleosomes on eukaryotic DNA and eukaryotic histones into nucleosomes on archaeal DNA at the same locations. T. kodakarensis has two histones, designated HTkA and HTkB, and strains with either but not both histones deleted grow normally but do exhibit transcriptome differences. Comparisons of the archaeal nucleosome profiles in the intergenic regions immediately upstream of genes that exhibited increased or decreased transcription in the absence of HTkA or HTkB revealed substantial differences but no consistent pattern of changes that would correlate directly with archaeal nucleosome positioning inhibiting or stimulating transcription. Conclusions The results obtained establish that an archaeal histone and a genome sequence together are sufficient to determine where archaeal nucleosomes preferentially assemble and where they avoid assembly. We confirm that the same nucleosome positioning code operates in Archaea as in Eukaryotes and presumably therefore evolved with the histone-fold mechanism of DNA binding and compaction early in the archaeal lineage, before the divergence of Eukaryotes.
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Affiliation(s)
- Narasimharao Nalabothula
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
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26
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An archaeal histone is required for transformation of Thermococcus kodakarensis. J Bacteriol 2012; 194:6864-74. [PMID: 23065975 DOI: 10.1128/jb.01523-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Archaeal histones wrap DNA into complexes, designated archaeal nucleosomes, that resemble the tetrasome core of a eukaryotic nucleosome. Therefore, all DNA interactions in vivo in Thermococcus kodakarensis, the most genetically versatile model species for archaeal research, must occur in the context of a histone-bound genome. Here we report the construction and properties of T. kodakarensis strains that have TK1413 or TK2289 deleted, the genes that encode HTkA and HTkB, respectively, the two archaeal histones present in this archaeon. All attempts to generate a strain with both TK1413 and TK2289 deleted were unsuccessful, arguing that a histone-mediated event(s) in T. kodakarensis is essential. The HTkA and HTkB amino acid sequences are 84% identical (56 of 67 residues) and 94% similar (63 of 67 residues), but despite this homology and their apparent redundancy in terms of supporting viability, the absence of HTkA and HTkB resulted in differences in growth and in quantitative and qualitative differences in genome transcription. A most surprising result was that the deletion of TK1413 (ΔhtkA) resulted in a T. kodakarensis strain that was no longer amenable to transformation, whereas the deletion of TK2289 (ΔhtkB) had no detrimental effects on transformation. Potential roles for the archaeal histones in regulating gene expression and for HTkA in DNA uptake and recombination are discussed.
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27
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Grohmann D, Werner F. Recent advances in the understanding of archaeal transcription. Curr Opin Microbiol 2011; 14:328-34. [DOI: 10.1016/j.mib.2011.04.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 04/13/2011] [Accepted: 04/13/2011] [Indexed: 01/12/2023]
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Transcriptional activation in the context of repression mediated by archaeal histones. Proc Natl Acad Sci U S A 2010; 107:6777-81. [PMID: 20351259 DOI: 10.1073/pnas.1002360107] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many archaea (including all the methanogens, nearly all euryarchaeotes, and some crenarchaeotes) use histones as components of the chromatin that compacts their genomes. The archaeal histones are homo- and heterodimers that pair on DNA to form tetrasomes (as the eukaryotic histones H3 and H4 do). The resulting DNA packaging is known to interfere with assembly of the archaeal transcription apparatus at promoters; the ability of transcriptional activation to function in repressive archaeal chromatin has not yet been explored in vitro. Using four of the Methanocaldococcus jannaschii (Mja) histones, we have examined activation of the model Mja rb2 transcription unit by the Mja transcriptional activator Ptr2 in this simplified-chromatin context. Using hydroxyl radical footprinting, we find that the Ptr2-specific rb2 upstream activating site is a preferred histone-localizing site that nucleates histone: DNA-binding radiating from the rb2 promoter. Nevertheless, Ptr2 competes effectively with histones for access to the rb2 promoter and most potently activates transcription in vitro at histone concentrations that extensively coat DNA and essentially silence basal transcription.
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29
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Daniels JP, Kelly S, Wickstead B, Gull K. Identification of a crenarchaeal orthologue of Elf1: implications for chromatin and transcription in Archaea. Biol Direct 2009; 4:24. [PMID: 19640276 PMCID: PMC2732611 DOI: 10.1186/1745-6150-4-24] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2009] [Accepted: 07/29/2009] [Indexed: 11/12/2022] Open
Abstract
The transcription machineries of Archaea and eukaryotes are similar in many aspects, but little is understood about archaeal chromatin and its role in transcription. Here, we describe the identification in hyperthermophilic Crenarchaeota and a Korarchaeon of an orthologue of the eukaryotic transcription elongation factor Elf1, which has been shown to function in chromatin structure maintenance of actively transcribed templates. Our discovery has implications for the relationship of chromatin and transcription in Archaea and the evolution of these processes in eukaryotes.
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Affiliation(s)
- Jan-Peter Daniels
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Steven Kelly
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Centre for Mathematical Biology, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB , UK
- Oxford Centre for Interactive Systems Biology, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Bill Wickstead
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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Abstract
NEQ288, one of two archaeal histones in Nanoarchaeum equitans, has a unique four-residue insertion that closely resembles an insertion in the eukaryotic histone H3 lineage. NEQ288 bound DNA but did not compact DNA in vitro in the absence of NEQ348, the second N. equitans archaeal histone. The properties of NEQ288 suggest an intermediate between the archaeal and H3 histone lineages and an evolutionary step toward the now-mandatory assembly of eukaryotic histones into heterodimers.
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31
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Abstract
Chromatin structure plays a vital role in the transmission of heritable gene expression patterns. The recent application of mass spectrometry to histone biology provides several striking insights into chromatin regulation. The continuing identification of new histone post-translational modifications is revolutionizing the ways in which we think about how access to genomic DNA is controlled. While post-translational modifications of the flexible histone tails continue to be an active area of investigation, the recent discovery of multiple modifications in the structured globular domains of histones provides new insights into how the nucleosome works. Recent experiments underscore the importance of a subgroup of these modifications: those that regulate histone-DNA interactions on the lateral surface of the nucleosome. This information highlights an emerging new paradigm in chromatin control, that of the epigenetic regulation of nucleosome mobility.
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Affiliation(s)
- Michael S Cosgrove
- Syracuse University, Department of Biology, Syracuse, New York, NY 13244, USA.
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32
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Abstract
The archaeal DNA replication machinery bears striking similarity to that of eukaryotes and is clearly distinct from the bacterial apparatus. In recent years, considerable advances have been made in understanding the biochemistry of the archaeal replication proteins. Furthermore, a number of structures have now been obtained for individual components and higher-order assemblies of archaeal replication factors, yielding important insights into the mechanisms of DNA replication in both archaea and eukaryotes.
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Affiliation(s)
- Elizabeth R Barry
- MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
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Santangelo TJ, Čuboňová L, James CL, Reeve JN. TFB1 or TFB2 is sufficient for Thermococcus kodakaraensis viability and for basal transcription in vitro. J Mol Biol 2006; 367:344-57. [PMID: 17275836 PMCID: PMC1855253 DOI: 10.1016/j.jmb.2006.12.069] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 12/22/2006] [Accepted: 12/27/2006] [Indexed: 11/18/2022]
Abstract
Archaeal RNA polymerases (RNAPs) are most similar to eukaryotic RNAP II (Pol II) but require the support of only two archaeal general transcription factors, TBP (TATA-box binding protein) and TFB (archaeal homologue of the eukaryotic general transcription factor TFIIB) to initiate basal transcription. However, many archaeal genomes encode more than one TFB and/or TBP leading to the hypothesis that different TFB/TBP combinations may be employed to direct initiation from different promoters in Archaea. As a first test of this hypothesis, we have determined the ability of RNAP purified from Thermococcus kodakaraensis (T.k.) to initiate transcription from a variety of T.k. promoters in vitro when provided with T.k. TBP and either TFB1 or TFB2, the two TFBs encoded in the T.k. genome. With every promoter active in vitro, transcription initiation occurred with either TFB1 or TFB2 although the optimum salt concentration for initiation was generally higher for TFB2 (approximately 250 mM K(+)) than for TFB1 (approximately 200 mM K(+)). Consistent with this functional redundancy in vitro, T.k. strains have been constructed with the TFB1- (tfb1; TK1280) or TFB2- (tfb2; TK2287) encoding gene deleted. These mutants exhibit no detectable growth defects under laboratory conditions. Domain swapping between TFB1 and TFB2 has identified a central region that contributes to the salt sensitivity of TFB activity, and deleting residues predicted to form the tip of the B-finger region of TFB2 had no detectable effects on promoter recognition or transcription initiation but did eliminate the production of very short (< or =5 nt) abortive transcripts.
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34
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Shin JH, Santangelo TJ, Xie Y, Reeve JN, Kelman Z. Archaeal minichromosome maintenance (MCM) helicase can unwind DNA bound by archaeal histones and transcription factors. J Biol Chem 2006; 282:4908-4915. [PMID: 17158792 DOI: 10.1074/jbc.m606847200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Protein-DNA complexes must be disassembled to facilitate DNA replication. Replication forks contain a helicase that unwinds the duplex DNA at the front of the fork. The minichromosome maintenance helicase from the archaeon Methanothermobacter thermautotrophicus required only ATP to unwind DNA bound into complexes by the M. thermautotrophicus archaeal histone HMtA2, transcription repressor TrpY, or into a transcription pre-initiation complex by M. thermautotrophicus TATA-box-binding protein, transcription factor B, and RNA polymerase. In contrast, the minichromosome maintenance helicase was unable to unwind DNA bound by this archaeal RNA polymerase in a stalled transcript-elongating complex.
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Affiliation(s)
- Jae-Ho Shin
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850 and the
| | | | - Yunwei Xie
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - John N Reeve
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - Zvi Kelman
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850 and the.
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Santangelo TJ, Reeve JN. Archaeal RNA polymerase is sensitive to intrinsic termination directed by transcribed and remote sequences. J Mol Biol 2005; 355:196-210. [PMID: 16305799 DOI: 10.1016/j.jmb.2005.10.062] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Revised: 10/26/2005] [Accepted: 10/26/2005] [Indexed: 11/15/2022]
Abstract
Archaea are prokaryotes with a single DNA-dependent RNA polymerase (RNAP) that is homologous to, and likely resembles the ancestor of all three eukaryotic RNAPs. In vitro studies have confirmed that initiation by archaeal RNAPs resembles the Pol II system, and we report the first detailed in vitro investigation of archaeal transcription termination. Methanothermobacter thermautotrophicus (M.t.) RNAP is susceptible to intrinsic termination at an intergenic sequence that conforms to a bacterial intrinsic terminator, as well as at bona fide bacterial intrinsic terminators. In contrast to bacterial RNAPs, M.t. RNAP also terminated in response to synthetic and natural oligo-T-rich sequences that were not preceded by sequences with any recognizable potential to form a stable RNA hairpin. Both template topology and temperature influenced the position and extent of termination in vitro, and the results argue that transcription of an upstream sequence can alter the termination response of the archaeal RNAP at a remote downstream sequence.
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Affiliation(s)
- Thomas J Santangelo
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
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Sandman K, Reeve JN. Archaeal chromatin proteins: different structures but common function? Curr Opin Microbiol 2005; 8:656-61. [PMID: 16256418 DOI: 10.1016/j.mib.2005.10.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Accepted: 10/11/2005] [Indexed: 10/25/2022]
Abstract
Chromatin proteins promote chromosome flexibility in vivo, maintaining a compact yet decondensed template that permits polymerase accessibility. All Archaea have at least two types of chromatin proteins, and diversity in the chromatin protein population appears to prevent polymerization of a single type of protein. Of the numerous chromatin proteins that have been described in Archaea, only two--histones and Alba homologs--are present in all archaeal phyla. Although their structures and complexes with DNA have no similarities, their functions probably overlap as mutants that lack single chromatin proteins are viable.
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Affiliation(s)
- Kathleen Sandman
- Department of Microbiology, Ohio State University, 484W. 12th Avenue, Columbus, OH 43210, USA.
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Xie Y, Reeve JN. Regulation of tryptophan operon expression in the archaeon Methanothermobacter thermautotrophicus. J Bacteriol 2005; 187:6419-29. [PMID: 16159776 PMCID: PMC1236654 DOI: 10.1128/jb.187.18.6419-6429.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 07/07/2005] [Indexed: 11/20/2022] Open
Abstract
Conserved trp genes encode enzymes that catalyze tryptophan biosynthesis in all three biological domains, and studies of their expression in Bacteria and eukaryotes have revealed a variety of different regulatory mechanisms. The results reported here provide the first detailed description of an archaeal trp gene regulatory system. We have established that the trpEGCFBAD operon in Methanothermobacter thermautotrophicus is transcribed divergently from a gene (designated trpY) that encodes a tryptophan-sensitive transcription regulator. TrpY binds to TRP box sequences (consensus, TGTACA) located in the overlapping promoter regions between trpY and trpE, inhibiting trpY transcription in the absence of tryptophan and both trpY and trpEGCFBAD transcription in the presence of tryptophan. TrpY apparently inhibits trpY transcription by blocking RNA polymerase access to the site of trpY transcription initiation and represses trpEGCFBAD transcription by preventing TATA box binding protein (TBP) binding to the TATA box sequence. Given that residue 2 (W2) is the only tryptophan in TrpY and in TrpY homologues in other Euryarchaea and that there is only one tryptophan codon in the entire trpEGCFBAD operon (trpB encodes W175), expression of the trp operon may also be regulated in vivo by the supply of charged tRNA(Trp) available to translate the second codon of the trpY mRNA.
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Affiliation(s)
- Yunwei Xie
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210-1292, USA
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Abstract
The relatively complex archaeal RNA polymerases are constructed along eukaryotic lines, and require two initiation factors for promoter recognition and specific transcription that are homologues of the RNA polymerase II TATA-binding protein and TFIIB. Many archaea also produce histones. In contrast, the transcriptional regulators encoded by archaeal genomes are primarily of bacterial rather than eukaryotic type. It is this combination of elements commonly regarded as separate and mutually exclusive that promises unifying insights into basic transcription mechanisms across all three domains of life.
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Affiliation(s)
- E Peter Geiduschek
- Division of Biological Sciences and Center for Molecular Genetics, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0634, USA
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Bell SD. Archaeal transcriptional regulation – variation on a bacterial theme? Trends Microbiol 2005; 13:262-5. [PMID: 15936657 DOI: 10.1016/j.tim.2005.03.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Revised: 03/17/2005] [Accepted: 03/31/2005] [Indexed: 10/25/2022]
Abstract
There is now an increasing body of data available on the DNA-binding properties of several putative transcriptional regulators in the Archaeal domain of life. The evidence points to simple models of promoter occlusion or facilitated recruitment of basal machinery for repressors and activators, respectively. However, little is known about the co-factor requirements, in vivo mechanisms and targets of many of these regulators. It is anticipated that the application of post-genomic technologies will begin to shed light on this fascinating area.
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Affiliation(s)
- Stephen D Bell
- MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge, CB2 2XZ, UK.
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Xie Y, Reeve JN. Transcription by Methanothermobacter thermautotrophicus RNA polymerase in vitro releases archaeal transcription factor B but not TATA-box binding protein from the template DNA. J Bacteriol 2004; 186:6306-10. [PMID: 15342601 PMCID: PMC515165 DOI: 10.1128/jb.186.18.6306-6310.2004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcription initiation in Archaea requires the assembly of a preinitiation complex containing the TATA- box binding protein (TBP), transcription factor B (TFB), and RNA polymerase (RNAP). The results reported establish the fate of Methanothermobacter thermautotrophicus TBP and TFB following transcription initiation by M. thermautotrophicus RNAP in vitro. TFB is released after initiation, during extension of the transcript from 4 to 24 nucleotides, but TBP remains bound to the template DNA. Regulation of archaeal transcription initiation by a repressor competition with TBP for TATA-box region binding must accommodate this observation.
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Affiliation(s)
- Yunwei Xie
- Department of Microbiology, Ohio State University, Columbus, OH 43210-1292, USA
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