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Kompaniiets D, Wang D, Yang Y, Hu Y, Liu B. Structure and molecular mechanism of bacterial transcription activation. Trends Microbiol 2024; 32:379-397. [PMID: 37903670 DOI: 10.1016/j.tim.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 11/01/2023]
Abstract
Transcription activation is an important checkpoint of regulation of gene expression which occurs in response to different intracellular and extracellular signals. The key elements in this signal transduction process are transcription activators, which determine when and how gene expression is activated. Recent structural studies on a considerable number of new transcription activation complexes (TACs) revealed the remarkable mechanistic diversity of transcription activation mediated by different factors, necessitating a review and re-evaluation of the transcription activation mechanisms. In this review, we present a comprehensive summary of transcription activation mechanisms and propose a new, elaborate, and systematic classification of transcription activation mechanisms, primarily based on the structural features of diverse TAC components.
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Affiliation(s)
- Dmytro Kompaniiets
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Dong Wang
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Yang Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Bin Liu
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
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Kompaniiets D, He L, Wang D, Zhou W, Yang Y, Hu Y, Liu B. Structural basis for transcription activation by the nitrate-responsive regulator NarL. Nucleic Acids Res 2024; 52:1471-1482. [PMID: 38197271 PMCID: PMC10853779 DOI: 10.1093/nar/gkad1231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 01/11/2024] Open
Abstract
Transcription activation is a crucial step of regulation during transcription initiation and a classic check point in response to different stimuli and stress factors. The Escherichia coli NarL is a nitrate-responsive global transcription factor that controls the expression of nearly 100 genes. However, the molecular mechanism of NarL-mediated transcription activation is not well defined. Here we present a cryo-EM structure of NarL-dependent transcription activation complex (TAC) assembled on the yeaR promoter at 3.2 Å resolution. Our structure shows that the NarL dimer binds at the -43.5 site of the promoter DNA with its C-terminal domain (CTD) not only binding to the DNA but also making interactions with RNA polymerase subunit alpha CTD (αCTD). The key role of these NarL-mediated interactions in transcription activation was further confirmed by in vivo and in vitro transcription assays. Additionally, the NarL dimer binds DNA in a different plane from that observed in the structure of class II TACs. Unlike the canonical class II activation mechanism, NarL does not interact with σ4, while RNAP αCTD is bound to DNA on the opposite side of NarL. Our findings provide a structural basis for detailed mechanistic understanding of NarL-dependent transcription activation on yeaR promoter and reveal a potentially novel mechanism of transcription activation.
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Affiliation(s)
- Dmytro Kompaniiets
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Lina He
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Wang
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Wei Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yang Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- Hubei JiangXia Laboratory, Wuhan 430071, China
| | - Bin Liu
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
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Wang D, Kompaniiets D, Hu Y, Liu B. Editorial: Transcription and its regulation in bacteria. Front Microbiol 2023; 14:1200443. [PMID: 37250044 PMCID: PMC10213650 DOI: 10.3389/fmicb.2023.1200443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/28/2023] [Indexed: 05/31/2023] Open
Affiliation(s)
- Dong Wang
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, United States
| | - Dmytro Kompaniiets
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, United States
| | - Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Bin Liu
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, United States
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Bu F, Kompaniiets D, Liu B. How to compile different types of structural visualizations in one panel. Trends Biochem Sci 2023; 48:303-304. [PMID: 36804038 DOI: 10.1016/j.tibs.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 02/18/2023]
Affiliation(s)
- Fan Bu
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA; Food, Nutrition, and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Dmytro Kompaniiets
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Bin Liu
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA.
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Cannone G, Kompaniiets D, Graham S, White MF, Spagnolo L. Structure of the Saccharolobus solfataricus type III-D CRISPR effector. Curr Res Struct Biol 2023; 5:100098. [PMID: 36843655 PMCID: PMC9945777 DOI: 10.1016/j.crstbi.2023.100098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/26/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
CRISPR-Cas is a prokaryotic adaptive immune system, classified into six different types, each characterised by a signature protein. Type III systems, classified based on the presence of a Cas10 subunit, are rather diverse multi-subunit assemblies with a range of enzymatic activities and downstream ancillary effectors. The broad array of current biotechnological CRISPR applications is mainly based on proteins classified as Type II, however recent developments established the feasibility and efficacy of multi-protein Type III CRISPR-Cas effector complexes as RNA-targeting tools in eukaryotes. The crenarchaeon Saccharolobus solfataricus has two type III system subtypes (III-B and III-D). Here, we report the cryo-EM structure of the Csm Type III-D complex from S. solfataricus (SsoCsm), which uses CRISPR RNA to bind target RNA molecules, activating the Cas10 subunit for antiviral defence. The structure reveals the complex organisation, subunit/subunit connectivity and protein/guide RNA interactions of the SsoCsm complex, one of the largest CRISPR effectors known.
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Affiliation(s)
- Giuseppe Cannone
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom
| | - Dmytro Kompaniiets
- School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Shirley Graham
- School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Malcolm F. White
- School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Laura Spagnolo
- School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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