1
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Blombach F, Werner F. Chromatin and gene regulation in archaea. Mol Microbiol 2024. [PMID: 39096085 DOI: 10.1111/mmi.15302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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 London, London, UK
| | - Finn Werner
- Division of Biosciences, RNAP Laboratory, Institute of Structural and Molecular Biology (ISMB), University College London, London, UK
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2
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Myers T, Dykstra CM. Teaching old dogs new tricks: genetic engineering methanogens. Appl Environ Microbiol 2024; 90:e0224723. [PMID: 38856201 PMCID: PMC11267900 DOI: 10.1128/aem.02247-23] [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: 06/11/2024] Open
Abstract
Methanogenic archaea, which are integral to global carbon and nitrogen cycling, currently face challenges in genetic manipulation due to unique physiology and limited genetic tools. This review provides a survey of current and past developments in the genetic engineering of methanogens, including selection and counterselection markers, reporter systems, shuttle vectors, mutagenesis methods, markerless genetic exchange, and gene expression control. This review discusses genetic tools and emphasizes challenges tied to tool scarcity for specific methanogenic species. Mutagenesis techniques for methanogens, including physicochemical, transposon-mediated, liposome-mediated mutagenesis, and natural transformation, are outlined, along with achievements and challenges. Markerless genetic exchange strategies, such as homologous recombination and CRISPR/Cas-mediated genome editing, are also detailed. Finally, the review concludes by examining the control of gene expression in methanogens. The information presented underscores the urgent need for refined genetic tools in archaeal research. Despite historical challenges, recent advancements, notably CRISPR-based systems, hold promise for overcoming obstacles, with implications for global health, agriculture, climate change, and environmental engineering. This comprehensive review aims to bridge existing gaps in the literature, guiding future research in the expanding field of archaeal genetic engineering.
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Affiliation(s)
- Tyler Myers
- Department of Civil, Construction and Environmental Engineering, San Diego State University, San Diego, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Christy M. Dykstra
- Department of Civil, Construction and Environmental Engineering, San Diego State University, San Diego, California, USA
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3
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Zhan Y, Grabbe F, Oberbeckmann E, Dienemann C, Cramer P. Three-step mechanism of promoter escape by RNA polymerase II. Mol Cell 2024; 84:1699-1710.e6. [PMID: 38604172 DOI: 10.1016/j.molcel.2024.03.016] [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: 10/02/2023] [Revised: 01/04/2024] [Accepted: 03/16/2024] [Indexed: 04/13/2024]
Abstract
The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase II (RNA Pol II) and initiation factors are broken to enable promoter escape. Here, we reconstitute RNA Pol II promoter escape in vitro and determine high-resolution structures of initially transcribing complexes containing 8-, 10-, and 12-nt ordered RNAs and two elongation complexes containing 14-nt RNAs. We suggest that promoter escape occurs in three major steps. First, the growing RNA displaces the B-reader element of the initiation factor TFIIB without evicting TFIIB. Second, the rewinding of the transcription bubble coincides with the eviction of TFIIA, TFIIB, and TBP. Third, the binding of DSIF and NELF facilitates TFIIE and TFIIH dissociation, establishing the paused elongation complex. This three-step model for promoter escape fills a gap in our understanding of the initiation-elongation transition of RNA Pol II transcription.
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Affiliation(s)
- Yumeng Zhan
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frauke Grabbe
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Elisa Oberbeckmann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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4
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Pilatowski-Herzing E, Samson RY, Takemata N, Badel C, Bohall PB, Bell SD. Capturing chromosome conformation in Crenarchaea. Mol Microbiol 2024:10.1111/mmi.15245. [PMID: 38404013 PMCID: PMC11344861 DOI: 10.1111/mmi.15245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
While there is a considerable body of knowledge regarding the molecular and structural biology and biochemistry of archaeal information processing machineries, far less is known about the nature of the substrate for these machineries-the archaeal nucleoid. In this article, we will describe recent advances in our understanding of the three-dimensional organization of the chromosomes of model organisms in the crenarchaeal phylum.
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Affiliation(s)
- Elyza Pilatowski-Herzing
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
- Biology Department, Indiana University, Bloomington, IN 47405, USA
| | - Rachel Y. Samson
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
- Biology Department, Indiana University, Bloomington, IN 47405, USA
| | - Naomichi Takemata
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
- Biology Department, Indiana University, Bloomington, IN 47405, USA
- Present address: Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Catherine Badel
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
- Biology Department, Indiana University, Bloomington, IN 47405, USA
- Present address: Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 CNRS, Université de Strasbourg, F-67000 Strasbourg, France
| | - Peter B. Bohall
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
- Biology Department, Indiana University, Bloomington, IN 47405, USA
| | - Stephen D. Bell
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
- Biology Department, Indiana University, Bloomington, IN 47405, USA
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5
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Blombach F, Sýkora M, Case J, Feng X, Baquero DP, Fouqueau T, Phung DK, Barker D, Krupovic M, She Q, Werner F. Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays. Nat Commun 2024; 15:1620. [PMID: 38388540 PMCID: PMC10883916 DOI: 10.1038/s41467-024-45728-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Abstract
CRISPR arrays form the physical memory of CRISPR adaptive immune systems by incorporating foreign DNA as spacers that are often AT-rich and derived from viruses. As promoter elements such as the TATA-box are AT-rich, CRISPR arrays are prone to harbouring cryptic promoters. Sulfolobales harbour extremely long CRISPR arrays spanning several kilobases, a feature that is accompanied by the CRISPR-specific transcription factor Cbp1. Aberrant Cbp1 expression modulates CRISPR array transcription, but the molecular mechanisms underlying this regulation are unknown. Here, we characterise the genome-wide Cbp1 binding at nucleotide resolution and characterise the binding motifs on distinct CRISPR arrays, as well as on unexpected non-canonical binding sites associated with transposons. Cbp1 recruits Cren7 forming together 'chimeric' chromatin-like structures at CRISPR arrays. We dissect Cbp1 function in vitro and in vivo and show that the third helix-turn-helix domain is responsible for Cren7 recruitment, and that Cbp1-Cren7 chromatinization plays a dual role in the transcription of CRISPR arrays. It suppresses spurious transcription from cryptic promoters within CRISPR arrays but enhances CRISPR RNA transcription directed from their cognate promoters in their leader region. Our results show that Cbp1-Cren7 chromatinization drives the productive expression of long CRISPR arrays.
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Affiliation(s)
- Fabian Blombach
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
| | - Michal Sýkora
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Jo Case
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Xu Feng
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute, Shandong University, Qingdao, 266237, PR China
| | - Diana P Baquero
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, F-75015, Paris, France
| | - Thomas Fouqueau
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Duy Khanh Phung
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Declan Barker
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, F-75015, Paris, France
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute, Shandong University, Qingdao, 266237, PR China
| | - Finn Werner
- RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
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6
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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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7
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Grünberger F, Schmid G, El Ahmad Z, Fenk M, Vogl K, Reichelt R, Hausner W, Urlaub H, Lenz C, Grohmann D. Uncovering the temporal dynamics and regulatory networks of thermal stress response in a hyperthermophile using transcriptomics and proteomics. mBio 2023; 14:e0217423. [PMID: 37843364 PMCID: PMC10746257 DOI: 10.1128/mbio.02174-23] [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: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE Extreme environments provide unique challenges for life, and the study of extremophiles can shed light on the mechanisms of adaptation to such conditions. Pyrococcus furiosus, a hyperthermophilic archaeon, is a model organism for studying thermal stress response mechanisms. In this study, we used an integrated analysis of RNA-sequencing and mass spectrometry data to investigate the transcriptomic and proteomic responses of P. furiosus to heat and cold shock stress and recovery. Our results reveal the rapid and dynamic changes in gene and protein expression patterns associated with these stress responses, as well as the coordinated regulation of different gene sets in response to different stressors. These findings provide valuable insights into the molecular adaptations that facilitate life in extreme environments and advance our understanding of stress response mechanisms in hyperthermophilic archaea.
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Affiliation(s)
- Felix Grünberger
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Georg Schmid
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Zubeir El Ahmad
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Martin Fenk
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Katharina Vogl
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Robert Reichelt
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Winfried Hausner
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Dina Grohmann
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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8
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Baes R, Grünberger F, Pyr dit Ruys S, Couturier M, De Keulenaer S, Skevin S, Van Nieuwerburgh F, Vertommen D, Grohmann D, Ferreira-Cerca S, Peeters E. Transcriptional and translational dynamics underlying heat shock response in the thermophilic crenarchaeon Sulfolobus acidocaldarius. mBio 2023; 14:e0359322. [PMID: 37642423 PMCID: PMC10653856 DOI: 10.1128/mbio.03593-22] [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: 12/24/2022] [Accepted: 06/29/2023] [Indexed: 08/31/2023] Open
Abstract
IMPORTANCE Heat shock response is the ability to respond adequately to sudden temperature increases that could be harmful for cellular survival and fitness. It is crucial for microorganisms living in volcanic hot springs that are characterized by high temperatures and large temperature fluctuations. In this study, we investigated how S. acidocaldarius, which grows optimally at 75°C, responds to heat shock by altering its gene expression and protein production processes. We shed light on which cellular processes are affected by heat shock and propose a hypothesis on underlying regulatory mechanisms. This work is not only relevant for the organism's lifestyle, but also with regard to its evolutionary status. Indeed, S. acidocaldarius belongs to the archaea, an ancient group of microbes that is more closely related to eukaryotes than to bacteria. Our study thus also contributes to a better understanding of the early evolution of heat shock response.
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Affiliation(s)
- Rani Baes
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Felix Grünberger
- Institute of Microbiology and Archaea Centre, Universität Regensburg, Regensburg, Germany
| | | | - Mohea Couturier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sarah De Keulenaer
- NXTGNT, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Sonja Skevin
- NXTGNT, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | | | - Didier Vertommen
- Institut de Duve, Université Catholique de Louvain, Brussels, Belgium
| | - Dina Grohmann
- Institute of Microbiology and Archaea Centre, Universität Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Cellular Biochemistry of Microorganisms, Biochemie III, Universität Regensburg, Regensburg, Germany
- Laboratoire de Biologie Structurale de la Cellule (BIOC), UMR 7654 -CNRS, Ecole polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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9
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Xu Q, Du Q, Gao J, Chen L, Dong X, Li J. A robust genetic toolbox for fine-tuning gene expression in the CO 2-Fixing methanogenic archaeon Methanococcus maripaludis. Metab Eng 2023; 79:130-145. [PMID: 37495072 DOI: 10.1016/j.ymben.2023.07.007] [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: 05/16/2023] [Revised: 07/12/2023] [Accepted: 07/23/2023] [Indexed: 07/28/2023]
Abstract
Libraries of well-characterized genetic elements for fine-tuning gene expression are essential for biological and biotechnological research and applications. The fast-growing and genetically tractable methanogen, Methanococcus maripaludis, is a promising host organism for biotechnological conversion of carbon dioxide and renewable hydrogen into fuels and value-added products, as well as fundamental biological studies of archaea. However, the lack of molecular tools for gene expression has hindered its application as a workhorse to fine-tune gene and metabolic pathway expressions. In this study, we developed a genetic toolbox, including libraries of promoters, ribosome binding sites (RBS), and neutral sites for chromosomal integration, to facilitate precise gene expression in M. maripaludis. We generated a promoter library consisting of 81 constitutive promoters with expression strengths spanning a ∼104-fold dynamic range. Importantly, we identified a base composition rule for strong archaeal promoters and successfully remodeled weak promoters, enhancing their activities by up to 120-fold. We also established an RBS library containing 42 diverse RBS sequences with translation strengths covering a ∼100-fold dynamic range. Additionally, we identified eight neutral sites and developed a one-step, Cas9-based marker-less knock-in approach for chromosomal integration. We successfully applied the characterized promoter and RBS elements to significantly improve recombinant protein expression by 41-fold and modulate essential gene expression to generate corresponding physiological changes in M. maripaludis. Therefore, this work establishes a solid foundation for utilizing this autotrophic methanogen as an ideal workhorse for archaeal biology and biotechnological studies and applications.
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Affiliation(s)
- Qing Xu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing Du
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, China
| | - Jian Gao
- School of Basic Medical Sciences and School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China.
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10
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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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11
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Sybers D, Charlier D, Peeters E. In Vitro Transcription Assay for Archaea Belonging to Sulfolobales. Methods Mol Biol 2022; 2516:81-102. [PMID: 35922623 DOI: 10.1007/978-1-0716-2413-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Archaeal transcription and its regulation are characterized by a mosaic of eukaryotic and bacterial features. Molecular analysis of the functioning of the archaeal RNA polymerase, basal transcription factors, and specific promoter-containing DNA templates allows to unravel the mechanisms of transcription regulation in archaea. In vitro transcription is a technique that allows the study of this process in a simplified and controlled environment less complex than the archaeal cell. In this chapter, we present an in vitro transcription methodology for the study of transcription in Sulfolobales. It is described how to purify the RNA polymerase and the basal transcription factors TATA-binding protein and transcription factor B of Saccharolobus solfataricus and how to perform in vitro transcription reactions and transcript detection. Application of this protocol for other archaeal species could require minor modifications to protein overexpression and purification conditions.
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Affiliation(s)
- David Sybers
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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12
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Li J, Yue L, Li Z, Zhang W, Zhang B, Zhao F, Dong X. aCPSF1 cooperates with terminator U-tract to dictate archaeal transcription termination efficacy. eLife 2021; 10:70464. [PMID: 34964713 PMCID: PMC8716108 DOI: 10.7554/elife.70464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/16/2021] [Indexed: 01/19/2023] Open
Abstract
Recently, aCPSF1 was reported to function as the long-sought global transcription termination factor of archaea; however, the working mechanism remains elusive. This work, through analyzing transcript-3′end-sequencing data of Methanococcus maripaludis, found genome-wide positive correlations of both the terminator uridine(U)-tract and aCPSF1 with hierarchical transcription termination efficacies (TTEs). In vitro assays determined that aCPSF1 specifically binds to the terminator U-tract with U-tract number-related binding affinity, and in vivo assays demonstrated the two elements are indispensable in dictating high TTEs, revealing that aCPSF1 and the terminator U-tract cooperatively determine high TTEs. The N-terminal KH domains equip aCPSF1 with specific-binding capacity to terminator U-tract and the aCPSF1-terminator U-tract cooperation; while the nuclease activity of aCPSF1 was also required for TTEs. aCPSF1 also guarantees the terminations of transcripts with weak intrinsic terminator signals. aCPSF1 orthologs from Lokiarchaeota and Thaumarchaeota exhibited similar U-tract cooperation in dictating TTEs. Therefore, aCPSF1 and the intrinsic U-rich terminator could work in a noteworthy two-in-one termination mode in archaea, which may be widely employed by archaeal phyla; using one trans-action factor to recognize U-rich terminator signal and cleave transcript 3′-end, the archaeal aCPSF1-dependent transcription termination may represent a simplified archetypal mode of the eukaryotic RNA polymerase II termination machinery.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lei Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhihua Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenting Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bing Zhang
- University of Chinese Academy of Sciences, Beijing, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Fangqing Zhao
- University of Chinese Academy of Sciences, Beijing, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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13
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Maruyama H, Nambu T, Mashimo C, Okinaga T, Takeyasu K. Single-Molecule/Cell Analyses Reveal Principles of Genome-Folding Mechanisms in the Three Domains of Life. Int J Mol Sci 2021; 22:13432. [PMID: 34948225 PMCID: PMC8707338 DOI: 10.3390/ijms222413432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 11/21/2022] Open
Abstract
Comparative structural/molecular biology by single-molecule analyses combined with single-cell dissection, mass spectroscopy, and biochemical reconstitution have been powerful tools for elucidating the mechanisms underlying genome DNA folding. All genomes in the three domains of life undergo stepwise folding from DNA to 30-40 nm fibers. Major protein players are histone (Eukarya and Archaea), Alba (Archaea), and HU (Bacteria) for fundamental structural units of the genome. In Euryarchaeota, a major archaeal phylum, either histone or HTa (the bacterial HU homolog) were found to wrap DNA. This finding divides archaea into two groups: those that use DNA-wrapping as the fundamental step in genome folding and those that do not. Archaeal transcription factor-like protein TrmBL2 has been suggested to be involved in genome folding and repression of horizontally acquired genes, similar to bacterial H-NS protein. Evolutionarily divergent SMC proteins contribute to the establishment of higher-order structures. Recent results are presented, including the use of Hi-C technology to reveal that archaeal SMC proteins are involved in higher-order genome folding, and the use of single-molecule tracking to reveal the detailed functions of bacterial and eukaryotic SMC proteins. Here, we highlight the similarities and differences in the DNA-folding mechanisms in the three domains of life.
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Affiliation(s)
- Hugo Maruyama
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Takayuki Nambu
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Chiho Mashimo
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Toshinori Okinaga
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Kunio Takeyasu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan;
- Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan
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14
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Kessler AC, Maraia RJ. The nuclear and cytoplasmic activities of RNA polymerase III, and an evolving transcriptome for surveillance. Nucleic Acids Res 2021; 49:12017-12034. [PMID: 34850129 PMCID: PMC8643620 DOI: 10.1093/nar/gkab1145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 12/23/2022] Open
Abstract
A 1969 report that described biochemical and activity properties of the three eukaryotic RNA polymerases revealed Pol III as highly distinguishable, even before its transcripts were identified. Now known to be the most complex, Pol III contains several stably-associated subunits referred to as built-in transcription factors (BITFs) that enable highly efficient RNA synthesis by a unique termination-associated recycling process. In vertebrates, subunit RPC7(α/β) can be of two forms, encoded by POLR3G or POLR3GL, with differential activity. Here we review promoter-dependent transcription by Pol III as an evolutionary perspective of eukaryotic tRNA expression. Pol III also provides nonconventional functions reportedly by promoter-independent transcription, one of which is RNA synthesis from DNA 3'-ends during repair. Another is synthesis of 5'ppp-RNA signaling molecules from cytoplasmic viral DNA in a pathway of interferon activation that is dysfunctional in immunocompromised patients with mutations in Pol III subunits. These unconventional functions are also reviewed, including evidence that link them to the BITF subunits. We also review data on a fraction of the human Pol III transcriptome that evolved to include vault RNAs and snaRs with activities related to differentiation, and in innate immune and tumor surveillance. The Pol III of higher eukaryotes does considerably more than housekeeping.
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Affiliation(s)
- Alan C Kessler
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892 USA
| | - Richard J Maraia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892 USA
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15
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Blombach F, Fouqueau T, Matelska D, Smollett K, Werner F. Promoter-proximal elongation regulates transcription in archaea. Nat Commun 2021; 12:5524. [PMID: 34535658 PMCID: PMC8448881 DOI: 10.1038/s41467-021-25669-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 08/25/2021] [Indexed: 01/17/2023] Open
Abstract
Recruitment of RNA polymerase and initiation factors to the promoter is the only known target for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation are involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Saccharolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.
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Affiliation(s)
- Fabian Blombach
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK.
| | - Thomas Fouqueau
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Dorota Matelska
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Katherine Smollett
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Finn Werner
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK.
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16
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Lewis AM, Recalde A, Bräsen C, Counts JA, Nussbaum P, Bost J, Schocke L, Shen L, Willard DJ, Quax TEF, Peeters E, Siebers B, Albers SV, Kelly RM. The biology of thermoacidophilic archaea from the order Sulfolobales. FEMS Microbiol Rev 2021; 45:fuaa063. [PMID: 33476388 PMCID: PMC8557808 DOI: 10.1093/femsre/fuaa063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.
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Affiliation(s)
- April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Alejandra Recalde
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Christopher Bräsen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Phillip Nussbaum
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Jan Bost
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Schocke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Tessa E F Quax
- Archaeal Virus–Host Interactions, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sonja-Verena Albers
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
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17
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Nottebaum S, Weinzierl ROJ. Transcribing Genes the Hard Way: In Vitro Reconstitution of Nanoarchaeal RNA Polymerase Reveals Unusual Active Site Properties. Front Mol Biosci 2021; 8:669314. [PMID: 34141723 PMCID: PMC8204694 DOI: 10.3389/fmolb.2021.669314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Nanoarchaea represent a highly diverged archaeal phylum that displays many unusual biological features. The Nanoarchaeum equitans genome encodes a complete set of RNA polymerase (RNAP) subunits and basal factors. Several of the standard motifs in the active center contain radical substitutions that are normally expected to render the polymerase catalytically inactive. Here we show that, despite these unusual features, a RNAP reconstituted from recombinant Nanoarchaeum subunits is transcriptionally active. Using a sparse-matrix high-throughput screening method we identified an atypical stringent requirement for fluoride ions to maximize its activity under in vitro transcription conditions.
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Affiliation(s)
- Sven Nottebaum
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Orthomol Pharmazeutische Vertriebs GmbH, Langenfeld, Germany
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18
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Brázda V, Bartas M, Bowater RP. Evolution of Diverse Strategies for Promoter Regulation. Trends Genet 2021; 37:730-744. [PMID: 33931265 DOI: 10.1016/j.tig.2021.04.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022]
Abstract
DNA is fundamentally important for all cellular organisms due to its role as a store of hereditary genetic information. The precise and accurate regulation of gene transcription depends primarily on promoters, which vary significantly within and between genomes. Some promoters are rich in specific types of bases, while others have more varied, complex sequence characteristics. However, it is not only base sequence but also epigenetic modifications and altered DNA structure that regulate promoter activity. Significantly, many promoters across all organisms contain sequences that can form intrastrand hairpins (cruciforms) or four-stranded structures (G-quadruplex or i-motif). In this review we integrate recent studies on promoter regulation that highlight the importance of DNA structure in the evolutionary adaptation of promoter sequences.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Richard P Bowater
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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19
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Yue L, Li J, Zhang B, Qi L, Li Z, Zhao F, Li L, Zheng X, Dong X. The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode. Nucleic Acids Res 2020; 48:9589-9605. [PMID: 32857850 PMCID: PMC7515710 DOI: 10.1093/nar/gkaa702] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/07/2020] [Accepted: 08/12/2020] [Indexed: 01/16/2023] Open
Abstract
Transcription termination defines accurate transcript 3′-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological significance of the newly identified general transcription termination factor of Archaea, the ribonuclease aCPSF1, and elucidated its 3′-end cleavage triggered termination mechanism. The depletion of Mmp-aCPSF1 in Methanococcus maripaludis caused a genome-wide transcription termination defect and disordered transcriptome. Transcript-3′end-sequencing revealed that transcriptions primarily terminate downstream of a uridine-rich motif where Mmp-aCPSF1 performed an endoribonucleolytic cleavage, and the endoribonuclease activity was determined to be essential to the in vivo transcription termination. Co-immunoprecipitation and chromatin-immunoprecipitation detected interactions of Mmp-aCPSF1 with RNA polymerase and chromosome. Phylogenetic analysis revealed that the aCPSF1 orthologs are ubiquitously distributed among the archaeal phyla, and two aCPSF1 orthologs from Lokiarchaeota and Thaumarchaeota could replace Mmp-aCPSF1 to terminate transcription of M. maripaludis. Therefore, the aCPSF1 dependent termination mechanism could be widely employed in Archaea, including Lokiarchaeota belonging to Asgard Archaea, the postulated archaeal ancestor of Eukaryotes. Strikingly, aCPSF1-dependent archaeal transcription termination reported here exposes a similar 3′-cleavage mode as the eukaryotic RNA polymerase II termination, thus would shed lights on understanding the evolutionary linking between archaeal and eukaryotic termination machineries.
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Affiliation(s)
- Lei Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhang
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihua Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Fangqing Zhao
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Lingyan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaowei Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China
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20
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A CRISPRi-dCas9 System for Archaea and Its Use To Examine Gene Function during Nitrogen Fixation by Methanosarcina acetivorans. Appl Environ Microbiol 2020; 86:AEM.01402-20. [PMID: 32826220 DOI: 10.1128/aem.01402-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/15/2020] [Indexed: 12/22/2022] Open
Abstract
CRISPR-based systems are emerging as the premier method to manipulate many cellular processes. In this study, a simple and efficient CRISPR interference (CRISPRi) system for targeted gene repression in archaea was developed. The Methanosarcina acetivorans CRISPR-Cas9 system was repurposed by replacing Cas9 with the catalytically dead Cas9 (dCas9) to generate a CRISPRi-dCas9 system for targeted gene repression. To test the utility of the system, genes involved in nitrogen (N2) fixation were targeted for dCas9-mediated repression. First, the nif operon (nifHI 1 I 2 DKEN) that encodes molybdenum nitrogenase was targeted by separate guide RNAs (gRNAs), one targeting the promoter and the other targeting nifD Remarkably, growth of M. acetivorans with N2 was abolished by dCas9-mediated repression of the nif operon with each gRNA. The abundance of nif transcripts was >90% reduced in both strains expressing the gRNAs, and NifD was not detected in cell lysate. Next, we targeted NifB, which is required for nitrogenase cofactor biogenesis. Expression of a gRNA targeting the coding sequence of NifB decreased nifB transcript abundance >85% and impaired but did not abolish growth of M. acetivorans with N2 Finally, to ascertain the ability to study gene regulation using CRISPRi-dCas9, nrpR1, encoding a subunit of the repressor of the nif operon, was targeted. The nrpR1 repression strain grew normally with N2 but had increased nif operon transcript abundance, consistent with NrpR1 acting as a repressor. These results highlight the utility of the system, whereby a single gRNA when expressed with dCas9 can block transcription of targeted genes and operons in M. acetivorans IMPORTANCE Genetic tools are needed to understand and manipulate the biology of archaea, which serve critical roles in the biosphere. Methanogenic archaea (methanogens) are essential for the biological production of methane, an intermediate in the global carbon cycle, an important greenhouse gas, and a biofuel. The CRISPRi-dCas9 system in the model methanogen Methanosarcina acetivorans is, to our knowledge, the first Cas9-based CRISPR interference system in archaea. Results demonstrate that the system is remarkably efficient in targeted gene repression and provide new insight into nitrogen fixation by methanogens, the only archaea with nitrogenase. Overall, the CRISPRi-dCas9 system provides a simple, yet powerful, genetic tool to control the expression of target genes and operons in methanogens.
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21
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Abstract
Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.
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Affiliation(s)
- Sara Osman
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
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22
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Bylino OV, Ibragimov AN, Shidlovskii YV. Evolution of Regulated Transcription. Cells 2020; 9:E1675. [PMID: 32664620 PMCID: PMC7408454 DOI: 10.3390/cells9071675] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
The genomes of all organisms abound with various cis-regulatory elements, which control gene activity. Transcriptional enhancers are a key group of such elements in eukaryotes and are DNA regions that form physical contacts with gene promoters and precisely orchestrate gene expression programs. Here, we follow gradual evolution of this regulatory system and discuss its features in different organisms. In eubacteria, an enhancer-like element is often a single regulatory element, is usually proximal to the core promoter, and is occupied by one or a few activators. Activation of gene expression in archaea is accompanied by the recruitment of an activator to several enhancer-like sites in the upstream promoter region. In eukaryotes, activation of expression is accompanied by the recruitment of activators to multiple enhancers, which may be distant from the core promoter, and the activators act through coactivators. The role of the general DNA architecture in transcription control increases in evolution. As a whole, it can be seen that enhancers of multicellular eukaryotes evolved from the corresponding prototypic enhancer-like regulatory elements with the gradually increasing genome size of organisms.
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Affiliation(s)
- Oleg V. Bylino
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
| | - Airat N. Ibragimov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Yulii V. Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
- I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya St., 119048 Moscow, Russia
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23
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Discovery of 20 novel ribosomal leader candidates in bacteria and archaea. BMC Microbiol 2020; 20:130. [PMID: 32448158 PMCID: PMC7247131 DOI: 10.1186/s12866-020-01823-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNAs perform many functions in addition to supplying coding templates, such as binding proteins. RNA-protein interactions are important in multiple processes in all domains of life, and the discovery of additional protein-binding RNAs expands the scope for studying such interactions. To find such RNAs, we exploited a form of ribosomal regulation. Ribosome biosynthesis must be tightly regulated to ensure that concentrations of rRNAs and ribosomal proteins (r-proteins) match. One regulatory mechanism is a ribosomal leader (r-leader), which is a domain in the 5' UTR of an mRNA whose genes encode r-proteins. When the concentration of one of these r-proteins is high, the protein binds the r-leader in its own mRNA, reducing gene expression and thus protein concentrations. To date, 35 types of r-leaders have been validated or predicted. RESULTS By analyzing additional conserved RNA structures on a multi-genome scale, we identified 20 novel r-leader structures. Surprisingly, these included new r-leaders in the highly studied organisms Escherichia coli and Bacillus subtilis. Our results reveal several cases where multiple unrelated RNA structures likely bind the same r-protein ligand, and uncover previously unknown r-protein ligands. Each r-leader consistently occurs upstream of r-protein genes, suggesting a regulatory function. That the predicted r-leaders function as RNAs is supported by evolutionary correlations in the nucleotide sequences that are characteristic of a conserved RNA secondary structure. The r-leader predictions are also consistent with the locations of experimentally determined transcription start sites. CONCLUSIONS This work increases the number of known or predicted r-leader structures by more than 50%, providing additional opportunities to study structural and evolutionary aspects of RNA-protein interactions. These results provide a starting point for detailed experimental studies.
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24
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Abstract
Messenger RNAs (mRNAs) consist of a coding region (open reading frame (ORF)) and two untranslated regions (UTRs), 5'UTR and 3'UTR. Ribosomes travel along the coding region, translating nucleotide triplets (called codons) to a chain of amino acids. The coding region was long believed to mainly encode the amino acid content of proteins, whereas regulatory signals reside in the UTRs and in other genomic regions. However, in recent years we have learned that the ORF is expansively populated with various regulatory signals, or codes, which are related to all gene expression steps and additional intracellular aspects. In this paper, we review the current knowledge related to overlapping codes inside the coding regions, such as the influence of synonymous codon usage on translation speed (and, in turn, the effect of translation speed on protein folding), ribosomal frameshifting, mRNA stability, methylation, splicing, transcription and more. All these codes come together and overlap in the ORF sequence, ensuring production of the right protein at the right time.
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Affiliation(s)
- Shaked Bergman
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
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25
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Sanders TJ, Wenck BR, Selan JN, Barker MP, Trimmer SA, Walker JE, Santangelo TJ. FttA is a CPSF73 homologue that terminates transcription in Archaea. Nat Microbiol 2020; 5:545-553. [PMID: 32094586 PMCID: PMC7103508 DOI: 10.1038/s41564-020-0667-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/06/2020] [Indexed: 12/23/2022]
Abstract
Regulated gene expression is largely achieved by controlling the activities of essential, multisubunit RNA polymerase transcription elongation complexes (TECs). The extreme stability required of TECs to processively transcribe large genomic regions necessitates robust mechanisms to terminate transcription. Efficient transcription termination is particularly critical for gene-dense bacterial and archaeal genomes1-3 in which continued transcription would necessarily transcribe immediately adjacent genes and result in conflicts between the transcription and replication apparatuses4-6; the coupling of transcription and translation7,8 would permit the loading of ribosomes onto aberrant transcripts. Only select sequences or transcription termination factors can disrupt the otherwise extremely stable TEC and we demonstrate that one of the last universally conserved archaeal proteins with unknown biological function is the Factor that terminates transcription in Archaea (FttA). FttA resolves the dichotomy of a prokaryotic gene structure (operons and polarity) and eukaryotic molecular homology (general transcription apparatus) that is observed in Archaea. This missing link between prokaryotic and eukaryotic transcription regulation provides the most parsimonious link to the evolution of the processing activities involved in RNA 3'-end formation in Eukarya.
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Affiliation(s)
- Travis J Sanders
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Breanna R Wenck
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Jocelyn N Selan
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Mathew P Barker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Stavros A Trimmer
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Julie E Walker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
- Watchmaker Genomics, Boulder, CO, USA
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
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The TK0271 Protein Activates Transcription of Aromatic Amino Acid Biosynthesis Genes in the Hyperthermophilic Archaeon Thermococcus kodakarensis. mBio 2019; 10:mBio.01213-19. [PMID: 31506306 PMCID: PMC6737238 DOI: 10.1128/mbio.01213-19] [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: 11/20/2022] Open
Abstract
The mechanisms of transcriptional regulation in archaea are still poorly understood. In this study, we identified a transcriptional regulator in the hyperthermophilic archaeon Thermococcus kodakarensis that activates the transcription of three operons involved in the biosynthesis of aromatic amino acids. The study represents one of only a few that identifies a regulator in Archaea that activates transcription. The results also imply that transcriptional regulation of genes with the same function is carried out by diverse mechanisms in the archaea, depending on the lineage. TrpY from Methanothermobacter thermautotrophicus is a regulator that inhibits transcription of the Trp biosynthesis (trp) operon. Here, we show that the TrpY homolog in Thermococcus kodakarensis is not involved in such regulation. There are 87 genes on the T. kodakarensis genome predicted to encode transcriptional regulators (TRs). By screening for TRs that specifically bind to the promoter of the trp operon of T. kodakarensis, we identified TK0271. The gene resides in the aro operon, responsible for the biosynthesis of chorismate, a precursor for Trp, Tyr, and Phe. TK0271 was expressed in Escherichia coli, and the protein, here designated Tar (Thermococcalesaromatic amino acid regulator), was purified. Tar specifically bound to the trp promoter with a dissociation constant (Kd) value of approximately 5 nM. Tar also bound to the promoters of the Tyr/Phe biosynthesis (tyr-phe) and aro operons. The protein recognized a palindromic sequence (TGGACA-N8-TGTCCA) conserved in these promoters. In vitro transcription assays indicated that Tar activates transcription from all three promoters. We cultivated T. kodakarensis in amino acid-based medium and found that transcript levels of the trp, tyr-phe, and aro operons increased in the absence of Trp, Tyr, or Phe. We further constructed a TK0271 gene disruption strain (ΔTK0271). Growth of ΔTK0271 was similar to that of the host strain in medium including Trp, Tyr, and Phe but was significantly impaired in the absence of any one of these amino acids. The results suggest that Tar is responsible for the transcriptional activation of aromatic amino acid biosynthesis genes in T. kodakarensis.
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Ebright RH, Werner F, Zhang X. RNA Polymerase Reaches 60: Transcription Initiation, Elongation, Termination, and Regulation in Prokaryotes. J Mol Biol 2019; 431:3945-3946. [PMID: 31356803 DOI: 10.1016/j.jmb.2019.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Richard H Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.
| | - Finn Werner
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
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