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Xiong Y, Han W, Xu C, Shi J, Wang L, Jin T, Jia Q, Lu Y, Hu S, Dou SX, Lin W, Strick TR, Wang S, Li M. Single-molecule reconstruction of eukaryotic factor-dependent transcription termination. Nat Commun 2024; 15:5113. [PMID: 38879529 PMCID: PMC11180205 DOI: 10.1038/s41467-024-49527-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/09/2024] [Indexed: 06/19/2024] Open
Abstract
Factor-dependent termination uses molecular motors to remodel transcription machineries, but the associated mechanisms, especially in eukaryotes, are poorly understood. Here we use single-molecule fluorescence assays to characterize in real time the composition and the catalytic states of Saccharomyces cerevisiae transcription termination complexes remodeled by Sen1 helicase. We confirm that Sen1 takes the RNA transcript as its substrate and translocates along it by hydrolyzing multiple ATPs to form an intermediate with a stalled RNA polymerase II (Pol II) transcription elongation complex (TEC). We show that this intermediate dissociates upon hydrolysis of a single ATP leading to dissociation of Sen1 and RNA, after which Sen1 remains bound to the RNA. We find that Pol II ends up in a variety of states: dissociating from the DNA substrate, which is facilitated by transcription bubble rewinding, being retained to the DNA substrate, or diffusing along the DNA substrate. Our results provide a complete quantitative framework for understanding the mechanism of Sen1-dependent transcription termination in eukaryotes.
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Affiliation(s)
- Ying Xiong
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
- School of Physics, University of Chinese Academy of Sciences, Beijing, China
| | - Weijing Han
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Jing Shi
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lisha Wang
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Taoli Jin
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Qi Jia
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Shuxin Hu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- School of Physics, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Lin
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China.
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Terence R Strick
- Institut de Biologie de l'Ecole Normale Supérieure, PSL Université, INSERM, CNRS, Paris, France.
- Equipe Labellisée de la Ligue Nationale Contre le Cancer, Paris, France.
| | - Shuang Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China.
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
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2
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Shi J, Feng Z, Song Q, Wang F, Zhang Z, Liu J, Li F, Wen A, Liu T, Ye Z, Zhang C, Das K, Wang S, Feng Y, Lin W. Structural and functional insights into transcription activation of the essential LysR-type transcriptional regulators. Protein Sci 2024; 33:e5012. [PMID: 38723180 PMCID: PMC11081524 DOI: 10.1002/pro.5012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024]
Abstract
The enormous LysR-type transcriptional regulators (LTTRs), which are diversely distributed amongst prokaryotes, play crucial roles in transcription regulation of genes involved in basic metabolic pathways, virulence and stress resistance. However, the precise transcription activation mechanism of these genes by LTTRs remains to be explored. Here, we determine the cryo-EM structure of a LTTR-dependent transcription activation complex comprising of Escherichia coli RNA polymerase (RNAP), an essential LTTR protein GcvA and its cognate promoter DNA. Structural analysis shows two N-terminal DNA binding domains of GcvA (GcvA_DBD) dimerize and engage the GcvA activation binding sites, presenting the -35 element for specific recognition with the conserved σ70R4. In particular, the versatile C-terminal domain of α subunit of RNAP directly interconnects with GcvA_DBD, σ70R4 and promoter DNA, providing more interfaces for stabilizing the complex. Moreover, molecular docking supports glycine as one potential inducer of GcvA, and single molecule photobleaching experiments kinetically visualize the occurrence of tetrameric GcvA-engaged transcription activation complex as suggested for the other LTTR homologs. Thus, a general model for tetrameric LTTR-dependent transcription activation is proposed. These findings will provide new structural and functional insights into transcription activation of the essential LTTRs.
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Affiliation(s)
- Jing Shi
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Zhenzhen Feng
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Qian Song
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Fulin Wang
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Zhipeng Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal UniversityGuangzhouGuangdongChina
- Guangdong Key Laboratory of Laser Life ScienceCollege of Biophotonics, South China Normal UniversityGuangzhouGuangdongChina
- Songshan Lake Materials LaboratoryDongguanGuangdongChina
| | - Jian Liu
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Fangfang Li
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Aijia Wen
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Tianyu Liu
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Zonghang Ye
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Chao Zhang
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Kalyan Das
- Rega Institute for Medical Research, Department of MicrobiologyImmunology and Transplantation, KU LeuvenLeuvenBelgium
| | - Shuang Wang
- Songshan Lake Materials LaboratoryDongguanGuangdongChina
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of Physics, Chinese Academy of SciencesBeijingChina
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Wei Lin
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiChina
- Nanjing Drum Tower Hospital Clinical College, Nanjing University of Chinese MedicineNanjingChina
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3
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Novelli M, Bolla JM. RND Efflux Pump Induction: A Crucial Network Unveiling Adaptive Antibiotic Resistance Mechanisms of Gram-Negative Bacteria. Antibiotics (Basel) 2024; 13:501. [PMID: 38927168 PMCID: PMC11200565 DOI: 10.3390/antibiotics13060501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
The rise of multi-drug-resistant (MDR) pathogenic bacteria presents a grave challenge to global public health, with antimicrobial resistance ranking as the third leading cause of mortality worldwide. Understanding the mechanisms underlying antibiotic resistance is crucial for developing effective treatments. Efflux pumps, particularly those of the resistance-nodulation-cell division (RND) superfamily, play a significant role in expelling molecules from bacterial cells, contributing to the emergence of multi-drug resistance. These are transmembrane transporters naturally produced by Gram-negative bacteria. This review provides comprehensive insights into the modulation of RND efflux pump expression in bacterial pathogens by numerous and common molecules (bile, biocides, pharmaceuticals, additives, plant extracts, etc.). The interplay between these molecules and efflux pump regulators underscores the complexity of antibiotic resistance mechanisms. The clinical implications of efflux pump induction by non-antibiotic compounds highlight the challenges posed to public health and the urgent need for further investigation. By addressing antibiotic resistance from multiple angles, we can mitigate its impact and preserve the efficacy of antimicrobial therapies.
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Affiliation(s)
- Marine Novelli
- Aix Marseille Univ, INSERM, SSA, MCT, 13385 Marseille, France;
- Université Paris Cité, CNRS, Biochimie des Protéines Membranaires, F-75005 Paris, France
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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] [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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Wang Y, Yang X, Yu F, Deng Z, Lin S, Zheng J. Structural and functional characterization of AfsR, an SARP family transcriptional activator of antibiotic biosynthesis in Streptomyces. PLoS Biol 2024; 22:e3002528. [PMID: 38427710 PMCID: PMC10936776 DOI: 10.1371/journal.pbio.3002528] [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: 09/21/2023] [Revised: 03/13/2024] [Accepted: 01/29/2024] [Indexed: 03/03/2024] Open
Abstract
Streptomyces antibiotic regulatory proteins (SARPs) are widely distributed activators of antibiotic biosynthesis. Streptomyces coelicolor AfsR is an SARP regulator with an additional nucleotide-binding oligomerization domain (NOD) and a tetratricopeptide repeat (TPR) domain. Here, we present cryo-electron microscopy (cryo-EM) structures and in vitro assays to demonstrate how the SARP domain activates transcription and how it is modulated by NOD and TPR domains. The structures of transcription initiation complexes (TICs) show that the SARP domain forms a side-by-side dimer to simultaneously engage the afs box overlapping the -35 element and the σHrdB region 4 (R4), resembling a sigma adaptation mechanism. The SARP extensively interacts with the subunits of the RNA polymerase (RNAP) core enzyme including the β-flap tip helix (FTH), the β' zinc-binding domain (ZBD), and the highly flexible C-terminal domain of the α subunit (αCTD). Transcription assays of full-length AfsR and truncated proteins reveal the inhibitory effect of NOD and TPR on SARP transcription activation, which can be eliminated by ATP binding. In vitro phosphorylation hardly affects transcription activation of AfsR, but counteracts the disinhibition of ATP binding. Overall, our results present a detailed molecular view of how AfsR serves to activate transcription.
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Affiliation(s)
- Yiqun Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Yu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
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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] [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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Lages MA, do Vale A, Lemos ML, Balado M. Remodulation of bacterial transcriptome after acquisition of foreign DNA: the case of irp-HPI high-pathogenicity island in Vibrio anguillarum. mSphere 2024; 9:e0059623. [PMID: 38078732 PMCID: PMC10826351 DOI: 10.1128/msphere.00596-23] [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: 10/11/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024] Open
Abstract
The high-pathogenicity island irp-HPI is widespread in Vibrionaceae and encodes the siderophore piscibactin, as well as the regulator PbtA that is essential for its expression. In this work, we aim to study whether PbtA directly interacts with irp-HPI promoters. Furthermore, we hypothesize that PbtA, and thereby the acquisition of irp-HPI island, may also influence the expression of other genes elsewhere in the bacterial genome. To address this question, an RNAseq analysis was conducted to identify differentially expressed genes after pbtA deletion in Vibrio anguillarum RV22 genetic background. The results showed that PbtA not only modulates the irp-HPI genes but also modulates the expression of a plethora of V. anguillarum core genome genes, inducing nitrate, arginine, and sulfate metabolism, T6SS1, and quorum sensing, while repressing lipopolysaccharide (LPS) production, MARTX toxin, and major porins such as OmpV and ChiP. The direct binding of the C-terminal domain of PbtA to piscibactin promoters (PfrpA and PfrpC), quorum sensing (vanT), LPS transporter wza, and T6SS structure- and effector-encoding genes was demonstrated by electrophoretic mobility shift assay (EMSA). The results provide valuable insights into the regulatory mechanisms underlying the expression of irp-HPI island and its impact on Vibrios transcriptome, with implications in pathogenesis.IMPORTANCEHorizontal gene transfer enables bacteria to acquire traits, such as virulence factors, thereby increasing the risk of the emergence of new pathogens. irp-HPI genomic island has a broad dissemination in Vibrionaceae and is present in numerous potentially pathogenic marine bacteria, some of which can infect humans. Previous works showed that certain V. anguillarum strains exhibit an expanded host range plasticity and heightened virulence, a phenomenon linked to the acquisition of the irp-HPI genomic island. The present work shows that this adaptive capability is likely achieved through comprehensive changes in the transcriptome of the bacteria and that these changes are mediated by the master regulator PbtA encoded within the irp-HPI element. Our results shed light on the broad implications of horizontal gene transfer in bacterial evolution, showing that the acquired DNA can directly mediate changes in the expression of the core genome, with profounds implications in pathogenesis.
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Affiliation(s)
- Marta A. Lages
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana do Vale
- Fish Immunology and Vaccinology Group, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Manuel L. Lemos
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Miguel Balado
- Department of Microbiology and Parasitology, Institute of Aquaculture, University of Santiago de Compostela, Santiago de Compostela, Spain
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Chubiz LM. The Mar, Sox, and Rob Systems. EcoSal Plus 2023; 11:eesp00102022. [PMID: 37220096 PMCID: PMC10729928 DOI: 10.1128/ecosalplus.esp-0010-2022] [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: 09/14/2022] [Accepted: 03/03/2023] [Indexed: 01/28/2024]
Abstract
Environments inhabited by Enterobacteriaceae are diverse and often stressful. This is particularly true for Escherichia coli and Salmonella during host association in the gastrointestinal systems of animals. There, E. coli and Salmonella must survive exposure to various antimicrobial compounds produced or ingested by their host. A myriad of changes to cellular physiology and metabolism are required to achieve this feat. A central regulatory network responsible for sensing and responding to intracellular chemical stressors like antibiotics are the Mar, Sox, and Rob systems found throughout the Enterobacteriaceae. Each of these distinct regulatory networks controls expression of an overlapping set of downstream genes whose collective effects result in increased resistance to a wide array of antimicrobial compounds. This collection of genes is known as the mar-sox-rob regulon. This review will provide an overview of the mar-sox-rob regulon and molecular architecture of the Mar, Sox, and Rob systems.
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Affiliation(s)
- Lon M. Chubiz
- Department of Biology, University of Missouri–St. Louis, St. Louis, Missouri, USA
- Biochemistry and Biotechnology Program, University of Missouri–St. Louis, St. Louis, Missouri, USA
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9
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Zhao M, Gao B, Wen A, Feng Y, Lu YQ. Structural basis of λCII-dependent transcription activation. Structure 2023; 31:968-974.e3. [PMID: 37269829 DOI: 10.1016/j.str.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 06/05/2023]
Abstract
The CII protein of bacteriophage λ activates transcription from the phage promoters PRE, PI, and PAQ by binding to two direct repeats that straddle the promoter -35 element. Although genetic, biochemical, and structural studies have elucidated many aspects of λCII-mediated transcription activation, no precise structure of the transcription machinery in the process is available. Here, we report a 3.1-Å cryo-electron microscopy (cryo-EM) structure of an intact λCII-dependent transcription activation complex (TAC-λCII), which comprises λCII, E. coli RNAP-σ70 holoenzyme, and the phage promoter PRE. The structure reveals the interactions between λCII and the direct repeats responsible for promoter specificity and the interactions between λCII and RNAP α subunit C-terminal domain responsible for transcription activation. We also determined a 3.4-Å cryo-EM structure of an RNAP-promoter open complex (RPo-PRE) from the same dataset. Structural comparison between TAC-λCII and RPo-PRE provides new insights into λCII-dependent transcription activation.
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Affiliation(s)
- Minxing Zhao
- Department of Emergency Medicine of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Bo Gao
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Aijia Wen
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Immunity and Inflammatory Diseases, Hangzhou 310058, China.
| | - Yuan-Qiang Lu
- Department of Emergency Medicine of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
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Shi J, Feng Z, Xu J, Li F, Zhang Y, Wen A, Wang F, Song Q, Wang L, Cui H, Tong S, Chen P, Zhu Y, Zhao G, Wang S, Feng Y, Lin W. Structural insights into the transcription activation mechanism of the global regulator GlnR from actinobacteria. Proc Natl Acad Sci U S A 2023; 120:e2300282120. [PMID: 37216560 PMCID: PMC10235972 DOI: 10.1073/pnas.2300282120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
In actinobacteria, an OmpR/PhoB subfamily protein called GlnR acts as an orphan response regulator and globally coordinates the expression of genes responsible for nitrogen, carbon, and phosphate metabolism in actinobacteria. Although many researchers have attempted to elucidate the mechanisms of GlnR-dependent transcription activation, progress is impeded by lacking of an overall structure of GlnR-dependent transcription activation complex (GlnR-TAC). Here, we report a co-crystal structure of the C-terminal DNA-binding domain of GlnR (GlnR_DBD) in complex with its regulatory cis-element DNA and a cryo-EM structure of GlnR-TAC which comprises Mycobacterium tuberculosis RNA polymerase, GlnR, and a promoter containing four well-characterized conserved GlnR binding sites. These structures illustrate how four GlnR protomers coordinate to engage promoter DNA in a head-to-tail manner, with four N-terminal receiver domains of GlnR (GlnR-RECs) bridging GlnR_DBDs and the RNAP core enzyme. Structural analysis also unravels that GlnR-TAC is stabilized by complex protein-protein interactions between GlnR and the conserved β flap, σAR4, αCTD, and αNTD domains of RNAP, which are further confirmed by our biochemical assays. Taken together, these results reveal a global transcription activation mechanism for the master regulator GlnR and other OmpR/PhoB subfamily proteins and present a unique mode of bacterial transcription regulation.
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Affiliation(s)
- Jing Shi
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
- Department of Biophysics, Zhejiang University School of Medicine, 310058Hangzhou, China
- Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058Hangzhou, China
| | - Zhenzhen Feng
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Juncao Xu
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032Shanghai, China
| | - Fangfang Li
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Yuqiong Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, 510631Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, 510631Guangzhou, Guangdong, China
- Songshan Lake Materials Laboratory, 523808Dongguan, Guangdong, China
| | - Aijia Wen
- Department of Biophysics, Zhejiang University School of Medicine, 310058Hangzhou, China
- Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058Hangzhou, China
| | - Fulin Wang
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Qian Song
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Lu Wang
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Hong Cui
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, 251000Soochow, China
| | - Shujuan Tong
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Peiying Chen
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Yejin Zhu
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032Shanghai, China
| | - Shuang Wang
- Songshan Lake Materials Laboratory, 523808Dongguan, Guangdong, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190Beijing, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, 310058Hangzhou, China
- Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058Hangzhou, China
| | - Wei Lin
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai200237, China
- Nanjing Drum Tower Hospital Clinical College, Nanjing University of Chinese Medicine, 210023Nanjing, China
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