1
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Chauvier A, Dandpat SS, Romero R, Walter NG. A nascent riboswitch helix orchestrates robust transcriptional regulation through signal integration. Nat Commun 2024; 15:3955. [PMID: 38729929 PMCID: PMC11087558 DOI: 10.1038/s41467-024-48409-8] [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: 01/09/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Widespread manganese-sensing transcriptional riboswitches effect the dependable gene regulation needed for bacterial manganese homeostasis in changing environments. Riboswitches - like most structured RNAs - are believed to fold co-transcriptionally, subject to both ligand binding and transcription events; yet how these processes are orchestrated for robust regulation is poorly understood. Through a combination of single-molecule and bulk approaches, we discover how a single Mn2+ ion and the transcribing RNA polymerase (RNAP), paused immediately downstream by a DNA template sequence, are coordinated by the bridging switch helix P1.1 in the representative Lactococcus lactis riboswitch. This coordination achieves a heretofore-overlooked semi-docked global conformation of the nascent RNA, P1.1 base pair stabilization, transcription factor NusA ejection, and RNAP pause extension, thereby enforcing transcription readthrough. Our work demonstrates how a central, adaptable RNA helix functions analogous to a molecular fulcrum of a first-class lever system to integrate disparate signals for finely balanced gene expression control.
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Affiliation(s)
- Adrien Chauvier
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Shiba S Dandpat
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
- Intel Corporation, Hillsboro, OR, USA
| | - Rosa Romero
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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2
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Said N, Finazzo M, Hilal T, Wang B, Selinger TL, Gjorgjevikj D, Artsimovitch I, Wahl MC. Sm-like protein Rof inhibits transcription termination factor ρ by binding site obstruction and conformational insulation. Nat Commun 2024; 15:3186. [PMID: 38622114 PMCID: PMC11018626 DOI: 10.1038/s41467-024-47439-6] [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: 09/08/2023] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Transcription termination factor ρ is a hexameric, RNA-dependent NTPase that can adopt active closed-ring and inactive open-ring conformations. The Sm-like protein Rof, a homolog of the RNA chaperone Hfq, inhibits ρ-dependent termination in vivo but recapitulation of this activity in vitro has proven difficult and the precise mode of Rof action is presently unknown. Here, our cryo-EM structures of ρ-Rof and ρ-RNA complexes show that Rof undergoes pronounced conformational changes to bind ρ at the protomer interfaces, undercutting ρ conformational dynamics associated with ring closure and occluding extended primary RNA-binding sites that are also part of interfaces between ρ and RNA polymerase. Consistently, Rof impedes ρ ring closure, ρ-RNA interactions and ρ association with transcription elongation complexes. Structure-guided mutagenesis coupled with functional assays confirms that the observed ρ-Rof interface is required for Rof-mediated inhibition of cell growth and ρ-termination in vitro. Bioinformatic analyses reveal that Rof is restricted to Pseudomonadota and that the ρ-Rof interface is conserved. Genomic contexts of rof differ between Enterobacteriaceae and Vibrionaceae, suggesting distinct modes of Rof regulation. We hypothesize that Rof and other cellular anti-terminators silence ρ under diverse, but yet to be identified, stress conditions when unrestrained transcription termination by ρ may be detrimental.
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Affiliation(s)
- Nelly Said
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany
| | - Mark Finazzo
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Tarek Hilal
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany
- Research Center of Electron Microscopy and Core Facility BioSupraMol, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstr. 36a, D-14195 Berlin, Germany
| | - Bing Wang
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Tim Luca Selinger
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany
| | - Daniela Gjorgjevikj
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany
- Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge CB2 0QH, United Kingdom
| | - Irina Artsimovitch
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany.
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, D-12489 Berlin, Germany.
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3
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Zuber PK, Said N, Hilal T, Wang B, Loll B, González-Higueras J, Ramírez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH. Concerted transformation of a hyper-paused transcription complex and its reinforcing protein. Nat Commun 2024; 15:3040. [PMID: 38589445 PMCID: PMC11001881 DOI: 10.1038/s41467-024-47368-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/28/2024] [Indexed: 04/10/2024] Open
Abstract
RfaH, a paralog of the universally conserved NusG, binds to RNA polymerases (RNAP) and ribosomes to activate expression of virulence genes. In free, autoinhibited RfaH, an α-helical KOW domain sequesters the RNAP-binding site. Upon recruitment to RNAP paused at an ops site, KOW is released and refolds into a β-barrel, which binds the ribosome. Here, we report structures of ops-paused transcription elongation complexes alone and bound to the autoinhibited and activated RfaH, which reveal swiveled, pre-translocated pause states stabilized by an ops hairpin in the non-template DNA. Autoinhibited RfaH binds and twists the ops hairpin, expanding the RNA:DNA hybrid to 11 base pairs and triggering the KOW release. Once activated, RfaH hyper-stabilizes the pause, which thus requires anti-backtracking factors for escape. Our results suggest that the entire RfaH cycle is solely determined by the ops and RfaH sequences and provide insights into mechanisms of recruitment and metamorphosis of NusG homologs across all life.
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Affiliation(s)
- Philipp K Zuber
- Biochemistry IV-Biophysical Chemistry, Universität Bayreuth, Bayreuth, Germany
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Nelly Said
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Tarek Hilal
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
- Research Center of Electron Microscopy and Core Facility BioSupraMol, Freie Universität Berlin, Berlin, Germany
| | - Bing Wang
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Bernhard Loll
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Jorge González-Higueras
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
| | | | - Irina Artsimovitch
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| | - Markus C Wahl
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany.
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany.
| | - Stefan H Knauer
- Biochemistry IV-Biophysical Chemistry, Universität Bayreuth, Bayreuth, Germany.
- Bristol-Myers Squibb GmbH & Co. KGaA, Munich, Germany.
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4
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El Sayyed H, Pambos OJ, Stracy M, Gottesman ME, Kapanidis AN. Single-molecule tracking reveals the functional allocation, in vivo interactions, and spatial organization of universal transcription factor NusG. Mol Cell 2024; 84:926-937.e4. [PMID: 38387461 DOI: 10.1016/j.molcel.2024.01.025] [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: 12/19/2022] [Revised: 12/14/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
During transcription elongation, NusG aids RNA polymerase by inhibiting pausing, promoting anti-termination on rRNA operons, coupling transcription with translation on mRNA genes, and facilitating Rho-dependent termination. Despite extensive work, the in vivo functional allocation and spatial distribution of NusG remain unknown. Using single-molecule tracking and super-resolution imaging in live E. coli cells, we found NusG predominantly in a chromosome-associated population (binding to RNA polymerase in elongation complexes) and a slowly diffusing population complexed with the 30S ribosomal subunit; the latter provides a "30S-guided" path for NusG into transcription elongation. Only ∼10% of NusG is fast diffusing, with its mobility suggesting non-specific interactions with DNA for >50% of the time. Antibiotic treatments and deletion mutants revealed that chromosome-associated NusG participates mainly in rrn anti-termination within phase-separated transcriptional condensates and in transcription-translation coupling. This study illuminates the multiple roles of NusG and offers a guide on dissecting multi-functional machines via in vivo imaging.
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Affiliation(s)
- Hafez El Sayyed
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK; Kavli Institute of Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford, UK.
| | - Oliver J Pambos
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK; Kavli Institute of Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford, UK
| | - Mathew Stracy
- Sir William Dunn School of Pathology, University of Oxford, South Parks Rd, Oxford, UK
| | - Max E Gottesman
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY, USA
| | - Achillefs N Kapanidis
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK; Kavli Institute of Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford, UK.
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5
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Ju X, Li S, Froom R, Wang L, Lilic M, Delbeau M, Campbell EA, Rock JM, Liu S. Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome. Nature 2024; 627:424-430. [PMID: 38418874 PMCID: PMC10937400 DOI: 10.1038/s41586-024-07105-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/23/2024] [Indexed: 03/02/2024]
Abstract
Mycobacterium tuberculosis (Mtb) is a bacterial pathogen that causes tuberculosis (TB), an infectious disease that is responsible for major health and economic costs worldwide1. Mtb encounters diverse environments during its life cycle and responds to these changes largely by reprogramming its transcriptional output2. However, the mechanisms of Mtb transcription and how they are regulated remain poorly understood. Here we use a sequencing method that simultaneously determines both termini of individual RNA molecules in bacterial cells3 to profile the Mtb transcriptome at high resolution. Unexpectedly, we find that most Mtb transcripts are incomplete, with their 5' ends aligned at transcription start sites and 3' ends located 200-500 nucleotides downstream. We show that these short RNAs are mainly associated with paused RNA polymerases (RNAPs) rather than being products of premature termination. We further show that the high propensity of Mtb RNAP to pause early in transcription relies on the binding of the σ-factor. Finally, we show that a translating ribosome promotes transcription elongation, revealing a potential role for transcription-translation coupling in controlling Mtb gene expression. In sum, our findings depict a mycobacterial transcriptome that prominently features incomplete transcripts resulting from RNAP pausing. We propose that the pausing phase constitutes an important transcriptional checkpoint in Mtb that allows the bacterium to adapt to environmental changes and could be exploited for TB therapeutics.
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Affiliation(s)
- Xiangwu Ju
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Ruby Froom
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Ling Wang
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Mirjana Lilic
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Madeleine Delbeau
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA.
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.
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6
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Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS. Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase. Proc Natl Acad Sci U S A 2024; 121:e2311480121. [PMID: 38354263 PMCID: PMC10895346 DOI: 10.1073/pnas.2311480121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/17/2024] [Indexed: 02/16/2024] Open
Abstract
Cyanobacteria and evolutionarily related chloroplasts of algae and plants possess unique RNA polymerases (RNAPs) with characteristics that distinguish them from canonical bacterial RNAPs. The largest subunit of cyanobacterial RNAP (cyRNAP) is divided into two polypeptides, β'1 and β'2, and contains the largest known lineage-specific insertion domain, Si3, located in the middle of the trigger loop and spanning approximately half of the β'2 subunit. In this study, we present the X-ray crystal structure of Si3 and the cryo-EM structures of the cyRNAP transcription elongation complex plus the NusG factor with and without incoming nucleoside triphosphate (iNTP) bound at the active site. Si3 has a well-ordered and elongated shape that exceeds the length of the main body of cyRNAP, fits into cavities of cyRNAP in the absence of iNTP bound at the active site and shields the binding site of secondary channel-binding proteins such as Gre and DksA. A small transition from the trigger loop to the trigger helix upon iNTP binding results in a large swing motion of Si3; however, this transition does not affect the catalytic activity of cyRNAP due to its minimal contact with cyRNAP, NusG, or DNA. This study provides a structural framework for understanding the evolutionary significance of these features unique to cyRNAP and chloroplast RNAP and may provide insights into the molecular mechanism of transcription in specific environment of photosynthetic organisms and organelle.
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Affiliation(s)
- M. Zuhaib Qayyum
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA16802
| | - Masahiko Imashimizu
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA16802
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba305-8565, Japan
| | - Miron Leanca
- The Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Rishi K. Vishwakarma
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA16802
| | - Amber Riaz-Bradley
- The Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Yulia Yuzenkova
- The Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Katsuhiko S. Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA16802
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7
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Walter N, Chauvier A, Dandpat S, Romero R. A nascent riboswitch helix orchestrates robust transcriptional regulation through signal integration. RESEARCH SQUARE 2024:rs.3.rs-3849447. [PMID: 38352525 PMCID: PMC10862961 DOI: 10.21203/rs.3.rs-3849447/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Widespread manganese-sensing transcriptional riboswitches effect the dependable gene regulation needed for bacterial manganese homeostasis in changing environments. Riboswitches - like most structured RNAs - are believed to fold co-transcriptionally, subject to both ligand binding and transcription events; yet how these processes are orchestrated for robust regulation is poorly understood. Through a combination of single molecule and bulk approaches, we discovered how a single Mn 2+ ion and the transcribing RNA polymerase (RNAP), paused immediately downstream by a DNA template sequence, are coordinated by the bridging switch helix P1.1 in the paradigmatic Lactococcus lactis riboswitch. This coordination achieves a heretofore-overlooked semi-docked global conformation of the nascent RNA, P1.1 base pair stabilization, transcription factor NusA ejection, and RNAP pause extension, thereby enforcing transcription readthrough. Our work demonstrates how a central, adaptable RNA helix functions analogous to a molecular fulcrum of a first-class lever system to integrate disparate signals for finely balanced gene expression control.
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8
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Bhardwaj K, Kalita A, Verma N, Prakash A, Thakur R, Dutta D. Rho-dependent termination enables cellular pH homeostasis. J Bacteriol 2024; 206:e0035623. [PMID: 38169297 PMCID: PMC10810219 DOI: 10.1128/jb.00356-23] [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: 10/28/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
The termination factor Rho, an ATP-dependent RNA translocase, preempts pervasive transcription processes, thereby rendering genome integrity in bacteria. Here, we show that the loss of Rho function raised the intracellular pH to >8.0 in Escherichia coli. The loss of Rho function upregulates tryptophanase-A (TnaA), an enzyme that catabolizes tryptophan to produce indole, pyruvate, and ammonia. We demonstrate that the enhanced TnaA function had produced the conjugate base ammonia, raising the cellular pH in the Rho-dependent termination defective strains. On the other hand, the constitutively overexpressed Rho lowered the cellular pH to about 6.2, independent of cellular ammonia levels. Since Rho overexpression may increase termination activities, the decrease in cellular pH could result from an excess H+ ion production during ATP hydrolysis by overproduced Rho. Furthermore, we performed in vivo termination assays to show that the efficiency of Rho-dependent termination was increased at both acidic and basic pH ranges. Given that the Rho level remained unchanged, the alkaline pH increases the termination efficiency by stimulating Rho's catalytic activity. We conducted the Rho-mediated RNA release assay from a stalled elongation complex to show an efficient RNA release at alkaline pH, compared to the neutral or acidic pH, that supports our in vivo observation. Whereas acidic pH appeared to increase the termination function by elevating the cellular level of Rho. This study is the first to link Rho function to the cellular pH homeostasis in bacteria. IMPORTANCE The current study shows that the loss or gain of Rho-dependent termination alkalizes or acidifies the cytoplasm, respectively. In the case of loss of Rho function, the tryptophanase-A enzyme is upregulated, and degrades tryptophan, producing ammonia to alkalize cytoplasm. We hypothesize that Rho overproduction by deleting its autoregulatory DNA portion increases termination function, causing excessive ATP hydrolysis to produce H+ ions and cytoplasmic acidification. Therefore, this study is the first to unravel a relationship between Rho function and intrinsic cellular pH homeostasis. Furthermore, the Rho level increases in the absence of autoregulation, causing cytoplasmic acidification. As intracellular pH plays a critical role in enzyme function, such a connection between Rho function and alkalization will have far-reaching implications for bacterial physiology.
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Affiliation(s)
- Kanika Bhardwaj
- CSIR Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Arunima Kalita
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Neha Verma
- CSIR Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Anand Prakash
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Ruchika Thakur
- CSIR Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Dipak Dutta
- CSIR Institute of Microbial Technology, Chandigarh, India
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9
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Pérez-Varela M, Singh R, Colquhoun JM, Starich OG, Tierney ARP, Tipton KA, Rather PN. Evidence for Rho-dependent control of a virulence switch in Acinetobacter baumannii. mBio 2024; 15:e0270823. [PMID: 38085026 PMCID: PMC10790780 DOI: 10.1128/mbio.02708-23] [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: 10/26/2023] [Accepted: 10/26/2023] [Indexed: 12/31/2023] Open
Abstract
IMPORTANCE Acinetobacter baumannii is a significant cause of infections in the healthcare setting. More recently, A. baumannii has been a leading cause of secondary bacterial pneumonia in patients infected with SARS-CoV-2 and the overall frequency of A. baumannii infection increased 78% during the COVID-19 pandemic. A. baumannii can exist in virulent or avirulent subpopulations and this interconversion is mediated by the expression of a family of TetR-type transcriptional regulators. In this study, we demonstrate that Rho is a key regulatory component in the expression of these TetR regulators. Overall, this study is the first to address a role for Rho in A. baumannii and provides additional evidence for the role of Rho in regulating diversity in bacterial subpopulations.
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Affiliation(s)
- María Pérez-Varela
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
| | - Raja Singh
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
| | - Jennifer M. Colquhoun
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
- Research Service, Atlanta VA Medical Center, Decatur, Georgia, USA
| | - Olivia G. Starich
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
| | - Aimee R. P. Tierney
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
| | - Kyle A. Tipton
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
| | - Philip N. Rather
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
- Research Service, Atlanta VA Medical Center, Decatur, Georgia, USA
- Emory Antibiotic Resistance Center, Emory University, Atlanta, Georgia, USA
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10
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Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS. Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575193. [PMID: 38260627 PMCID: PMC10802570 DOI: 10.1101/2024.01.11.575193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cyanobacteria and evolutionarily related chloroplasts of algae and plants possess unique RNA polymerases (RNAPs) with characteristics that distinguish from canonical bacterial RNAPs. The largest subunit of cyanobacterial RNAP (cyRNAP) is divided into two polypeptides, β'1 and β'2, and contains the largest known lineage-specific insertion domain, Si3, located in the middle of the trigger loop and spans approximately half of the β'2 subunit. In this study, we present the X-ray crystal structure of Si3 and the cryo-EM structures of the cyRNAP transcription elongation complex plus the NusG factor with and without incoming nucleoside triphosphate (iNTP) bound at the active site. Si3 has a well-ordered and elongated shape that exceeds the length of the main body of cyRNAP, fits into cavities of cyRNAP and shields the binding site of secondary channel-binding proteins such as Gre and DksA. A small transition from the trigger loop to the trigger helix upon iNTP binding at the active site results in a large swing motion of Si3; however, this transition does not affect the catalytic activity of cyRNAP due to its minimal contact with cyRNAP, NusG or DNA. This study provides a structural framework for understanding the evolutionary significance of these features unique to cyRNAP and chloroplast RNAP and may provide insights into the molecular mechanism of transcription in specific environment of photosynthetic organisms.
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Affiliation(s)
- M. Zuhaib Qayyum
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Current address: Protein Technologies Center, Inspiration4 Advanced Research Center, Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Masahiko Imashimizu
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8565 Japan
| | - Miron Leanca
- The Centre for Bacterial Cell Biology, Newcastle University, UK
| | - Rishi K. Vishwakarma
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Yulia Yuzenkova
- The Centre for Bacterial Cell Biology, Newcastle University, UK
| | - Katsuhiko S. Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802, USA
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11
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Hurst MN, Beebout CJ, Hollingsworth A, Guckes KR, Purcell A, Bermudez TA, Williams D, Reasoner SA, Trent MS, Hadjifrangiskou M. The QseB response regulator imparts tolerance to positively charged antibiotics by controlling metabolism and minor changes to LPS. mSphere 2023; 8:e0005923. [PMID: 37676915 PMCID: PMC10597456 DOI: 10.1128/msphere.00059-23] [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: 02/01/2023] [Accepted: 06/02/2023] [Indexed: 09/09/2023] Open
Abstract
The modification of lipopolysaccharide (LPS) in Escherichia coli and Salmonella spp. is primarily controlled by the two-component system PmrAB. LPS modification allows bacteria to avoid killing by positively charged antibiotics like polymyxin B (PMB). We previously demonstrated that in uropathogenic E. coli (UPEC), the sensor histidine kinase PmrB also activates a non-cognate transcription factor, QseB, and this activation somehow augments PMB tolerance in UPEC. Here, we demonstrate-for the first time-that in the absence of the canonical LPS transcriptional regulator, PmrA, QseB can direct some modifications on the LPS. In agreement with this observation, transcriptional profiling analyses demonstrate regulatory overlaps between PmrA and QseB in terms of regulating LPS modification genes. However, both PmrA and QseB must be present for UPEC to mount robust tolerance to PMB. Transcriptional and metabolomic analyses also reveal that QseB transcriptionally regulates the metabolism of glutamate and 2-oxoglutarate, which are consumed and produced during the modification of lipid A. We show that deletion of qseB alters glutamate levels in the bacterial cells. The qseB deletion mutant, which is susceptible to positively charged antibiotics, is rescued by exogenous addition of 2-oxoglutarate. These findings uncover a previously unknown mechanism of metabolic control of antibiotic tolerance that may be contributing to antibiotic treatment failure in the clinic. IMPORTANCE Although antibiotic prescriptions are guided by well-established susceptibility testing methods, antibiotic treatments oftentimes fail. The presented work is significant because it uncovers a mechanism by which bacteria transiently avoid killing by antibiotics. This mechanism involves two closely related transcription factors, PmrA and QseB, which are conserved across Enterobacterales. We demonstrate that PmrA and QseB share regulatory targets in lipid A modification pathway and prove that QseB can orchestrate modifications of lipid A in Escherichia coli in the absence of PmrA. Finally, we show that QseB controls glutamate metabolism during the antibiotic response. These results suggest that rewiring of QseB-mediated metabolic genes could lead to stable antibiotic resistance in subpopulations within the host, thereby contributing to antibiotic treatment failure.
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Affiliation(s)
- Melanie N. Hurst
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Connor J. Beebout
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexis Hollingsworth
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Kirsten R. Guckes
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexandria Purcell
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Tomas A. Bermudez
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Diamond Williams
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Seth A. Reasoner
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Maria Hadjifrangiskou
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, Tennessee, USA
- Center for Personalized Microbiology, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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12
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Said N, Finazzo M, Hilal T, Wang B, Selinger TL, Gjorgjevikj D, Artsimovitch I, Wahl MC. Sm-like protein Rof inhibits transcription termination factor ρ by binding site obstruction and conformational insulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555460. [PMID: 37693585 PMCID: PMC10491184 DOI: 10.1101/2023.08.30.555460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Transcription termination factor ρ is a hexameric, RNA-dependent NTPase that can adopt active closed-ring and inactive open-ring conformations. The Sm-like protein Rof, a homolog of the RNA chaperone Hfq, inhibits ρ-dependent termination in vivo but recapitulation of this activity in vitro has proven difficult and the precise mode of Rof action is presently unknown. Our electron microscopic structures of ρ-Rof and ρ-RNA complexes show that Rof undergoes pronounced conformational changes to bind ρ at the protomer interfaces, undercutting ρ conformational dynamics associated with ring closure and occluding extended primary RNA-binding sites that are also part of interfaces between ρ and RNA polymerase. Consistently, Rof impedes ρ ring closure, ρ-RNA interactions, and ρ association with transcription elongation complexes. Structure-guided mutagenesis coupled with functional assays confirmed that the observed ρ-Rof interface is required for Rof-mediated inhibition of cell growth and ρ-termination in vitro. Bioinformatic analyses revealed that Rof is restricted to Pseudomonadota and that the ρ-Rof interface is conserved. Genomic contexts of rof differ between Enterobacteriaceae and Vibrionaceae, suggesting distinct modes of Rof regulation. We hypothesize that Rof and other cellular anti-terminators silence ρ under diverse, but yet to be identified, stress conditions when unrestrained transcription termination by ρ would be lethal.
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Affiliation(s)
- Nelly Said
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
| | - Mark Finazzo
- The Ohio State University, Department of Microbiology and Center for RNA Biology, Columbus, OH, USA
| | - Tarek Hilal
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy and Core Facility BioSupraMol, Fabeckstr. 36a, 14195 Berlin, Germany
| | - Bing Wang
- The Ohio State University, Department of Microbiology and Center for RNA Biology, Columbus, OH, USA
| | - Tim Luca Selinger
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
| | - Daniela Gjorgjevikj
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
| | - Irina Artsimovitch
- The Ohio State University, Department of Microbiology and Center for RNA Biology, Columbus, OH, USA
| | - Markus C. Wahl
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
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13
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Wang B, Said N, Hilal T, Finazzo M, Wahl MC, Artsimovitch I. Transcription termination factor ρ polymerizes under stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.18.553922. [PMID: 37645988 PMCID: PMC10462130 DOI: 10.1101/2023.08.18.553922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Bacterial RNA helicase ρ is a genome sentinel that terminates synthesis of damaged and junk RNAs that are not translated by the ribosome. Co-transcriptional RNA surveillance by ρ is essential for quality control of the transcriptome during optimal growth. However, it is unclear how bacteria protect their RNAs from overzealous ρ during dormancy or stress, conditions common in natural habitats. Here we used cryogenic electron microscopy, biochemical, and genetic approaches to show that residue substitutions, ADP, or ppGpp promote hyper-oligomerization of Escherichia coli ρ. Our results demonstrate that nucleotides bound at subunit interfaces control ρ switching from active hexamers to inactive higher-order oligomers and extended filaments. Polymers formed upon exposure to antibiotics or ppGpp disassemble when stress is relieved, thereby directly linking termination activity to cellular physiology. Inactivation of ρ through hyper-oligomerization is a regulatory strategy shared by RNA polymerases, ribosomes, and metabolic enzymes across all life.
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Affiliation(s)
- Bing Wang
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Nelly Said
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
| | - Tarek Hilal
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy and Core Facility BioSupraMol, Fabeckstr. 36a, 14195 Berlin, Germany
| | - Mark Finazzo
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Markus C. Wahl
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Irina Artsimovitch
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
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14
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Yakhnin A, Bubunenko M, Mandell Z, Lubkowska L, Husher S, Babitzke P, Kashlev M. Robust regulation of transcription pausing in Escherichia coli by the ubiquitous elongation factor NusG. Proc Natl Acad Sci U S A 2023; 120:e2221114120. [PMID: 37276387 PMCID: PMC10268239 DOI: 10.1073/pnas.2221114120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
Transcription elongation by multi-subunit RNA polymerases (RNAPs) is regulated by auxiliary factors in all organisms. NusG/Spt5 is the only universally conserved transcription elongation factor shared by all domains of life. NusG is a component of antitermination complexes controlling ribosomal RNA operons, an essential antipausing factor, and a transcription-translation coupling factor in Escherichia coli. We employed RNET-seq for genome-wide mapping of RNAP pause sites in wild-type and NusG-depleted cells. We demonstrate that NusG is a major antipausing factor that suppresses thousands of backtracked and nonbacktracked pauses across the E. coli genome. The NusG-suppressed pauses were enriched immediately downstream from the translation start codon but were also abundant elsewhere in open reading frames, small RNA genes, and antisense transcription units. This finding revealed a strong similarity of NusG to Spt5, which stimulates the elongation rate of many eukaryotic genes. We propose a model in which promoting forward translocation and/or stabilization of RNAP in the posttranslocation register by NusG results in suppression of pausing in E. coli.
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Affiliation(s)
- Alexander V. Yakhnin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Mikhail Bubunenko
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Zachary F. Mandell
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA16802
| | - Lucyna Lubkowska
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Sara Husher
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA16802
| | - Mikhail Kashlev
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
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15
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Ziegler CA, Freddolino PL. Escherichia coli Leucine-Responsive Regulatory Protein Bridges DNA In Vivo and Tunably Dissociates in the Presence of Exogenous Leucine. mBio 2023; 14:e0269022. [PMID: 36786566 PMCID: PMC10127797 DOI: 10.1128/mbio.02690-22] [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: 09/29/2022] [Accepted: 01/17/2023] [Indexed: 02/15/2023] Open
Abstract
Feast-famine response proteins are a widely conserved class of global regulators in prokaryotes, the most highly studied of which is the Escherichia coli leucine-responsive regulatory protein (Lrp). Lrp senses the environmental nutrition status and subsequently regulates up to one-third of the genes in E. coli, either directly or indirectly. Lrp exists predominantly as octamers and hexadecamers (16mers), where leucine is believed to shift the equilibrium toward the octameric state. In this study, we analyzed the effects of three oligomerization state mutants of Lrp in terms of their ability to bind to DNA and regulate gene expression in response to exogenous leucine. We find that oligomerization beyond dimers is required for Lrp's regulatory activity and that, contrary to previous speculation, exogenous leucine modulates Lrp activity at its target promoters exclusively by inhibiting Lrp binding to DNA. We also show evidence that Lrp binding bridges DNA over length scales of multiple kilobases, revealing a new range of mechanisms for Lrp-mediated transcriptional regulation. IMPORTANCE Leucine-responsive regulatory protein (Lrp) is one of the most impactful regulators in E. coli and other bacteria. Lrp senses nutrient conditions and responds by controlling strategies for virulence, cellular motility, and nutrient acquisition. Despite its importance and being evolutionarily highly conserved across bacteria and archaea, several mysteries remain regarding Lrp, including how it actually responds to leucine to change its regulation of targets. Previous studies have led to the hypothesis that Lrp switches between two states, an octamer (8 Lrp molecules together) and a hexadecamer (16 Lrp molecules together), upon exposure to leucine; these are referred to as different oligomerization states. Here, we show that contrary to previous expectations, it is Lrp's propensity to bind DNA, rather than its oligomerization state, that is directly affected by leucine in the cell's environment. Our new understanding of Lrp activity will aid in identifying and disrupting pathways used by bacteria to cause disease.
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Affiliation(s)
- Christine A. Ziegler
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
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16
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Ahmad E, Mitra A, Ahmed W, Mahapatra V, Hegde SR, Sala C, Cole ST, Nagaraja V. Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194923. [PMID: 36822574 DOI: 10.1016/j.bbagrm.2023.194923] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/31/2023] [Accepted: 02/14/2023] [Indexed: 02/24/2023]
Abstract
Intrinsic and Rho-dependent transcription termination mechanisms regulate gene expression and recycle RNA polymerase in bacteria. Both the modes are well studied in Escherichia coli, and a few other organisms. The understanding of Rho function is limited in most other bacteria including mycobacteria. Here, we highlight the dominance of Rho-dependent termination in mycobacteria and validate Rho as a key regulatory factor. The lower abundance of intrinsic terminators, high cellular levels of Rho, and its genome-wide association with a majority of transcriptionally active genes indicate the pronounced role of Rho-mediated termination in Mycobacterium tuberculosis (Mtb). Rho modulates the termination of RNA synthesis for both protein-coding and stable RNA genes in Mtb. Concordantly, the depletion of Rho in mycobacteria impact its growth and enhances the transcription read-through at 3' ends of the transcription units. We demonstrate that MtbRho is catalytically active in the presence of RNA with varied secondary structures. These properties suggest an evolutionary adaptation of Rho as the efficient and preponderant mode of transcription termination in mycobacteria.
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Affiliation(s)
- Ezaz Ahmad
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Anirban Mitra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Wareed Ahmed
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Varsha Mahapatra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Shubhada R Hegde
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, India
| | - Claudia Sala
- Monoclonal Antibody Discovery Laboratory, Fondazione Toscana Life Sciences, 53100 Siena, Italy
| | | | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India.
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17
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Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase. Proc Natl Acad Sci U S A 2023; 120:e2218516120. [PMID: 36745813 PMCID: PMC9963633 DOI: 10.1073/pnas.2218516120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
NusG is a transcription elongation factor that stimulates transcription pausing in Gram+ bacteria including B. subtilis by sequence-specific interaction with a conserved pause-inducing -11TTNTTT-6 motif found in the non-template DNA (ntDNA) strand within the transcription bubble. To reveal the structural basis of NusG-dependent pausing, we determined a cryo-EM structure of a paused transcription complex (PTC) containing RNA polymerase (RNAP), NusG, and the TTNTTT motif in the ntDNA strand. The interaction of NusG with the ntDNA strand rearranges the transcription bubble by positioning three consecutive T residues in a cleft between NusG and the β-lobe domain of RNAP. We revealed that the RNAP swivel module rotation (swiveling), which widens (swiveled state) and narrows (non-swiveled state) a cleft between NusG and the β-lobe, is an intrinsic motion of RNAP and is directly linked to trigger loop (TL) folding, an essential conformational change of all cellular RNAPs for the RNA synthesis reaction. We also determined cryo-EM structures of RNAP escaping from the paused transcription state. These structures revealed the NusG-dependent pausing mechanism by which NusG-ntDNA interaction inhibits the transition from swiveled to non-swiveled states, thereby preventing TL folding and RNA synthesis allosterically. This motion is also reduced by the formation of an RNA hairpin within the RNA exit channel. Thus, the pause half-life can be modulated by the strength of the NusG-ntDNA interaction and/or the stability of the RNA hairpin. NusG residues that interact with the TTNTTT motif are widely conserved in bacteria, suggesting that NusG-dependent pausing is widespread.
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18
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Hurst MN, Beebout CJ, Hollingsworth A, Guckes KR, Purcell A, Bermudez TA, Williams D, Reasoner SA, Trent MS, Hadjifrangiskou M. The QseB response regulator imparts tolerance to positively charged antibiotics by controlling metabolism and minor changes to LPS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523522. [PMID: 36711705 PMCID: PMC9882033 DOI: 10.1101/2023.01.10.523522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The modification of lipopolysaccharide (LPS) in Escherichia coli and Salmonella spp . is primarily controlled by the two-component system PmrAB. LPS modification allows bacteria to avoid killing by positively charged antibiotics like polymyxin B. We previously demonstrated that in uropathogenic E. coli (UPEC), the sensor histidine kinase PmrB also activates a non-cognate transcription factor, QseB, and this activation somehow augments polymyxin B tolerance in UPEC. Here, we demonstrate - for the first time - that in the absence of the canonical LPS transcriptional regulator, PmrA, QseB can direct some modifications on the LPS. In agreement with this observation, transcriptional profiling analyses demonstrate regulatory overlaps between PmrA and QseB in terms of regulating LPS modification genes. However, both PmrA and QseB must be present for UPEC to mount robust tolerance to polymyxin B. Transcriptional and metabolomic analyses also reveal that QseB transcriptionally regulates the metabolism of glutamate and 2-oxoglutarate, which are consumed and produced during the modification of lipid A. We show that deletion of qseB alters glutamate levels in the bacterial cells. The qseB deletion mutant, which is susceptible to positively charged antibiotics, is rescued by exogenous addition of 2-oxoglutarate. These findings uncover a previously unknown mechanism of metabolic control of antibiotic tolerance that may be contributing to antibiotic treatment failure in the clinic. IMPORTANCE Although antibiotic prescriptions are guided by well-established susceptibility testing methods, antibiotic treatments oftentimes fail. The presented work is significant, because it uncovers a mechanism by which bacteria transiently avoid killing by antibiotics. This mechanism involves two closely related transcription factors, PmrA and QseB, which are conserved across Enterobacteriaceae. We demonstrate that PmrA and QseB share regulatory targets in lipid A modification pathway and prove that QseB can orchestrate modifications of lipid A in E. coli in the absence of PmrA. Finally, we show that QseB controls glutamate metabolism during the antibiotic response. These results suggest that rewiring of QseB-mediated metabolic genes can lead to stable antibiotic resistance in subpopulations within the host, thereby contributing to antibiotic treatment failure.
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Affiliation(s)
- Melanie N. Hurst
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Connor J. Beebout
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Kirsten R. Guckes
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alexandria Purcell
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Tomas A. Bermudez
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Diamond Williams
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Seth A. Reasoner
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Maria Hadjifrangiskou
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology & Inflammation, Nashville, TN, USA
- Center for Personalized Microbiology, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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19
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Li X, Chou T. Stochastic dynamics and ribosome-RNAP interactions in transcription-translation coupling. Biophys J 2023; 122:254-266. [PMID: 36199250 PMCID: PMC9822797 DOI: 10.1016/j.bpj.2022.09.041] [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: 06/23/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 01/11/2023] Open
Abstract
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such transcription-translation coupling (TTC) has been evoked as a mechanism that speeds up the overall process, provides protection against premature termination, and/or regulates the timing of transcript and protein formation. What molecular mechanisms underlie ribosome-RNAP coupling and how they can perform these functions have not been explicitly modeled. We develop and analyze a continuous-time stochastic model that incorporates ribosome and RNAP elongation rates, initiation and termination rates, RNAP pausing, and direct ribosome and RNAP interactions (exclusion and binding). Our model predicts how distributions of delay times depend on these molecular features of transcription and translation. We also propose additional measures for TTC: a direct ribosome-RNAP binding probability and the fraction of time the translation-transcription process is "protected" from attack by transcription-terminating proteins. These metrics quantify different aspects of TTC and differentially depend on parameters of known molecular processes. We use our metrics to reveal how and when our model can exhibit either acceleration or deceleration of transcription, as well as protection from termination. Our detailed mechanistic model provides a basis for designing new experimental assays that can better elucidate the mechanisms of TTC.
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Affiliation(s)
- Xiangting Li
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California
| | - Tom Chou
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California; Department of Mathematics, University of California, Los Angeles, Los Angeles, California.
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20
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Ellinger E, Chauvier A, Romero RA, Liu Y, Ray S, Walter NG. Riboswitches as therapeutic targets: promise of a new era of antibiotics. Expert Opin Ther Targets 2023; 27:433-445. [PMID: 37364239 PMCID: PMC10527229 DOI: 10.1080/14728222.2023.2230363] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/13/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
INTRODUCTION The growth of antibiotic resistance among bacterial pathogens is an impending global threat that can only be averted through the development of novel antibacterial drugs. A promising answer could be the targeting of riboswitches, structured RNA elements found almost exclusively in bacteria. AREAS COVERED This review examines the potential of riboswitches as novel antibacterial drug targets. The limited mechanisms of action of currently available antibiotics are summarized, followed by a delineation of the functional mechanisms of riboswitches. We then discuss the potential for developing novel approaches that target paradigmatic riboswitches in the context of their bacterial gene expression machinery. EXPERT OPINION We highlight potential advantages of targeting riboswitches in their functional form, embedded within gene expression complexes critical for bacterial survival. We emphasize the benefits of this approach, including potentially higher species specificity and lower side effects.
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Affiliation(s)
- Emily Ellinger
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Adrien Chauvier
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Rosa A. Romero
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Yichen Liu
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Sujay Ray
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Nils G. Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
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21
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RfaH Counter-Silences Inhibition of Transcript Elongation by H-NS-StpA Nucleoprotein Filaments in Pathogenic Escherichia coli. mBio 2022; 13:e0266222. [PMID: 36264101 PMCID: PMC9765446 DOI: 10.1128/mbio.02662-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression of virulence genes in pathogenic Escherichia coli is controlled in part by the transcription silencer H-NS and its paralogs (e.g., StpA), which sequester DNA in multi-kb nucleoprotein filaments to inhibit transcription initiation, elongation, or both. Some activators counter-silence initiation by displacing H-NS from promoters, but how H-NS inhibition of elongation is overcome is not understood. In uropathogenic E. coli (UPEC), elongation regulator RfaH aids expression of some H-NS-silenced pathogenicity operons (e.g., hlyCABD encoding hemolysin). RfaH associates with elongation complexes (ECs) via direct contacts to a transiently exposed, nontemplate DNA strand sequence called operon polarity suppressor (ops). RfaH-ops interactions establish long-lived RfaH-EC contacts that allow RfaH to recruit ribosomes to the nascent mRNA and to suppress transcriptional pausing and termination. Using ChIP-seq, we mapped the genome-scale distributions of RfaH, H-NS, StpA, RNA polymerase (RNAP), and σ70 in the UPEC strain CFT073. We identify eight RfaH-activated operons, all of which were bound by H-NS and StpA. Four are new additions to the RfaH regulon. Deletion of RfaH caused premature termination, whereas deletion of H-NS and StpA allowed elongation without RfaH. Thus, RfaH is an elongation counter-silencer of H-NS. Consistent with elongation counter-silencing, deletion of StpA alone decreased the effect of RfaH. StpA increases DNA bridging, which inhibits transcript elongation via topological constraints on RNAP. Residual RfaH effect when both H-NS and StpA were deleted was attributable to targeting of RfaH-regulated operons by a minor H-NS paralog, Hfp. These operons have evolved higher levels of H-NS-binding features, explaining minor-paralog targeting. IMPORTANCE Bacterial pathogens adapt to hosts and host defenses by reprogramming gene expression, including by H-NS counter-silencing. Counter-silencing turns on transcription initiation when regulators bind to promoters and rearrange repressive H-NS nucleoprotein filaments that ordinarily block transcription. The specialized NusG paralog RfaH also reprograms virulence genes but regulates transcription elongation. To understand how elongation regulators might affect genes silenced by H-NS, we mapped H-NS, StpA (an H-NS paralog), RfaH, σ70, and RNA polymerase (RNAP) locations on DNA in the uropathogenic E. coli strain CFT073. Although H-NS-StpA filaments bind only 18% of the CFT073 genome, all loci at which RfaH binds RNAP are also bound by H-NS-StpA and are silenced when RfaH is absent. Thus, RfaH represents a distinct class of counter-silencer that acts on elongating RNAP to enable transcription through repressive nucleoprotein filaments. Our findings define a new mechanism of elongation counter-silencing and explain how RfaH functions as a virulence regulator.
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Abstract
In bacteria, transcription and translation take place in the same cellular compartment. Therefore, a messenger RNA can be translated as it is being transcribed, a process known as transcription-translation coupling. This process was already recognized at the dawn of molecular biology, yet the interplay between the two key players, the RNA polymerase and ribosome, remains elusive. Genetic data indicate that an RNA sequence can be translated shortly after it has been transcribed. The closer both processes are in time, the less accessible the RNA sequence is between the RNA polymerase and ribosome. This temporal coupling has important consequences for gene regulation. Biochemical and structural studies have detailed several complexes between the RNA polymerase and ribosome. The in vivo relevance of this physical coupling has not been formally demonstrated. We discuss how both temporal and physical coupling may mesh to produce the phenomenon we know as transcription-translation coupling.
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Affiliation(s)
- Gregor M Blaha
- Department of Biochemistry, University of California, Riverside, California, USA;
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA;
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
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23
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Artsimovitch I, Ramírez-Sarmiento CA. Metamorphic proteins under a computational microscope: Lessons from a fold-switching RfaH protein. Comput Struct Biotechnol J 2022; 20:5824-5837. [PMID: 36382197 PMCID: PMC9630627 DOI: 10.1016/j.csbj.2022.10.024] [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: 08/22/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/28/2022] Open
Abstract
Metamorphic proteins constitute unexpected paradigms of the protein folding problem, as their sequences encode two alternative folds, which reversibly interconvert within biologically relevant timescales to trigger different cellular responses. Once considered a rare aberration, metamorphism may be common among proteins that must respond to rapidly changing environments, exemplified by NusG-like proteins, the only transcription factors present in every domain of life. RfaH, a specialized paralog of bacterial NusG, undergoes an all-α to all-β domain switch to activate expression of virulence and conjugation genes in many animal and plant pathogens and is the quintessential example of a metamorphic protein. The dramatic nature of RfaH structural transformation and the richness of its evolutionary history makes for an excellent model for studying how metamorphic proteins switch folds. Here, we summarize the structural and functional evidence that sparked the discovery of RfaH as a metamorphic protein, the experimental and computational approaches that enabled the description of the molecular mechanism and refolding pathways of its structural interconversion, and the ongoing efforts to find signatures and general properties to ultimately describe the protein metamorphome.
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Affiliation(s)
- Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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24
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Structural basis of transcriptional regulation by a nascent RNA element, HK022 putRNA. Nat Commun 2022; 13:4668. [PMID: 35970830 PMCID: PMC9378689 DOI: 10.1038/s41467-022-32315-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/26/2022] [Indexed: 12/16/2022] Open
Abstract
Transcription, in which RNA polymerases (RNAPs) produce RNA from DNA, is the first step of gene expression. As such, it is highly regulated either by trans-elements like protein factors and/or by cis-elements like specific sequences on the DNA. Lambdoid phage HK022 contains a cis-element, put, which suppresses pausing and termination during transcription of the early phage genes. The putRNA transcript solely performs the anti-pausing/termination activities by interacting directly with the E.coli RNAP elongation complex (EC) by an unknown structural mechanism. In this study, we reconstituted putRNA-associated ECs and determined the structures using cryo-electron microscopy. The determined structures of putRNA-associated EC, putRNA-absent EC, and σ70-bound EC suggest that the putRNA interaction with the EC counteracts swiveling, a conformational change previously identified to promote pausing and σ70 might modulate putRNA folding via σ70-dependent pausing during elongation.
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25
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Interaction between transcribing RNA polymerase and topoisomerase I prevents R-loop formation in E. coli. Nat Commun 2022; 13:4524. [PMID: 35927234 PMCID: PMC9352719 DOI: 10.1038/s41467-022-32106-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 07/15/2022] [Indexed: 12/30/2022] Open
Abstract
Bacterial topoisomerase I (TopoI) removes excessive negative supercoiling and is thought to relax DNA molecules during transcription, replication and other processes. Using ChIP-Seq, we show that TopoI of Escherichia coli (EcTopoI) is colocalized, genome-wide, with transcribing RNA polymerase (RNAP). Treatment with transcription elongation inhibitor rifampicin leads to EcTopoI relocation to promoter regions, where RNAP also accumulates. When a 14 kDa RNAP-binding EcTopoI C-terminal domain (CTD) is overexpressed, colocalization of EcTopoI and RNAP along the transcription units is reduced. Pull-down experiments directly show that the two enzymes interact in vivo. Using ChIP-Seq and Topo-Seq, we demonstrate that EcTopoI is enriched upstream (within up to 12-15 kb) of highly-active transcription units, indicating that EcTopoI relaxes negative supercoiling generated by transcription. Uncoupling of the RNAP:EcTopoI interaction by either overexpression of EcTopoI competitor (CTD or inactive EcTopoI Y319F mutant) or deletion of EcTopoI domains involved in the interaction is toxic for cells and leads to excessive negative plasmid supercoiling. Moreover, uncoupling of the RNAP:EcTopoI interaction leads to R-loops accumulation genome-wide, indicating that this interaction is required for prevention of R-loops formation. In E. coli, disruption of TopoI and RNAP interaction decreases cells viability and leads to hypernegative DNA supercoiling and R loops accumulation. TopoI and DNA gyrase bind around transcription units and TopoI recognizes cleavage sites by a specific motif and negative supercoiling.
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26
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Molina JA, Galaz-Davison P, Komives EA, Artsimovitch I, Ramírez-Sarmiento CA. Allosteric couplings upon binding of RfaH to transcription elongation complexes. Nucleic Acids Res 2022; 50:6384-6397. [PMID: 35670666 PMCID: PMC9226497 DOI: 10.1093/nar/gkac453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/07/2022] [Accepted: 05/18/2022] [Indexed: 12/03/2022] Open
Abstract
In every domain of life, NusG-like proteins bind to the elongating RNA polymerase (RNAP) to support processive RNA synthesis and to couple transcription to ongoing cellular processes. Structures of factor-bound transcription elongation complexes (TECs) reveal similar contacts to RNAP, consistent with a shared mechanism of action. However, NusG homologs differ in their regulatory roles, modes of recruitment, and effects on RNA synthesis. Some of these differences could be due to conformational changes in RNAP and NusG-like proteins, which cannot be captured in static structures. Here, we employed hydrogen-deuterium exchange mass spectrometry to investigate changes in local and non-local structural dynamics of Escherichia coli NusG and its paralog RfaH, which have opposite effects on expression of xenogenes, upon binding to TEC. We found that NusG and RfaH regions that bind RNAP became solvent-protected in factor-bound TECs, whereas RNAP regions that interact with both factors showed opposite deuterium uptake changes when bound to NusG or RfaH. Additional changes far from the factor-binding site were observed only with RfaH. Our results provide insights into differences in structural dynamics exerted by NusG and RfaH during binding to TEC, which may explain their different functional outcomes and allosteric regulation of transcriptional pausing by RfaH.
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Affiliation(s)
- José Alejandro Molina
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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27
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Pukhrambam C, Molodtsov V, Kooshkbaghi M, Tareen A, Vu H, Skalenko KS, Su M, Yin Z, Winkelman JT, Kinney JB, Ebright RH, Nickels BE. Structural and mechanistic basis of σ-dependent transcriptional pausing. Proc Natl Acad Sci U S A 2022; 119:e2201301119. [PMID: 35653571 PMCID: PMC9191641 DOI: 10.1073/pnas.2201301119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/26/2022] [Indexed: 12/20/2022] Open
Abstract
In σ-dependent transcriptional pausing, the transcription initiation factor σ, translocating with RNA polymerase (RNAP), makes sequence-specific protein–DNA interactions with a promoter-like sequence element in the transcribed region, inducing pausing. It has been proposed that, in σ-dependent pausing, the RNAP active center can access off-pathway “backtracked” states that are substrates for the transcript-cleavage factors of the Gre family and on-pathway “scrunched” states that mediate pause escape. Here, using site-specific protein–DNA photocrosslinking to define positions of the RNAP trailing and leading edges and of σ relative to DNA at the λPR′ promoter, we show directly that σ-dependent pausing in the absence of GreB in vitro predominantly involves a state backtracked by 2–4 bp, and σ-dependent pausing in the presence of GreB in vitro and in vivo predominantly involves a state scrunched by 2–3 bp. Analogous experiments with a library of 47 (∼16,000) transcribed-region sequences show that the state scrunched by 2–3 bp—and only that state—is associated with the consensus sequence, T−3N−2Y−1G+1, (where −1 corresponds to the position of the RNA 3′ end), which is identical to the consensus for pausing in initial transcription and which is related to the consensus for pausing in transcription elongation. Experiments with heteroduplex templates show that sequence information at position T−3 resides in the DNA nontemplate strand. A cryoelectron microscopy structure of a complex engaged in σ-dependent pausing reveals positions of DNA scrunching on the DNA nontemplate and template strands and suggests that position T−3 of the consensus sequence exerts its effects by facilitating scrunching.
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Affiliation(s)
- Chirangini Pukhrambam
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
| | - Vadim Molodtsov
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Mahdi Kooshkbaghi
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Ammar Tareen
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Hoa Vu
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
| | - Kyle S. Skalenko
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
| | - Min Su
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Zhou Yin
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Jared T. Winkelman
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Justin B. Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Richard H. Ebright
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Bryce E. Nickels
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
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28
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Rho-dependent transcription termination proceeds via three routes. Nat Commun 2022; 13:1663. [PMID: 35351884 PMCID: PMC8964686 DOI: 10.1038/s41467-022-29321-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 03/09/2022] [Indexed: 01/26/2023] Open
Abstract
Rho is a general transcription termination factor in bacteria, but many aspects of its mechanism of action are unclear. Diverse models have been proposed for the initial interaction between the RNA polymerase (RNAP) and Rho (catch-up and stand-by pre-terminational models); for the terminational release of the RNA transcript (RNA shearing, RNAP hyper-translocation or displacing, and allosteric models); and for the post-terminational outcome (whether the RNAP dissociates or remains bound to the DNA). Here, we use single-molecule fluorescence assays to study those three steps in transcription termination mediated by E. coli Rho. We find that different mechanisms previously proposed for each step co-exist, but apparently occur on various timescales and tend to lead to specific outcomes. Our results indicate that three kinetically distinct routes take place: (1) the catch-up mode leads first to RNA shearing for RNAP recycling on DNA, and (2) later to RNAP displacement for decomposition of the transcriptional complex; (3) the last termination usually follows the stand-by mode with displacing for decomposing. This three-route model would help reconcile current controversies on the mechanisms. Rho is a general transcription termination factor in bacteria. Here, Song et al. use single-molecule fluorescence assays to provide evidence that Rho-mediated transcription termination can occur via three kinetically different routes.
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29
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Zhu C, Guo X, Dumas P, Takacs M, Abdelkareem M, Vanden Broeck A, Saint-André C, Papai G, Crucifix C, Ortiz J, Weixlbaumer A. Transcription factors modulate RNA polymerase conformational equilibrium. Nat Commun 2022; 13:1546. [PMID: 35318334 PMCID: PMC8940904 DOI: 10.1038/s41467-022-29148-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/01/2022] [Indexed: 01/26/2023] Open
Abstract
RNA polymerase (RNAP) frequently pauses during the transcription of DNA to RNA to regulate gene expression. Transcription factors NusA and NusG modulate pausing, have opposing roles, but can bind RNAP simultaneously. Here we report cryo-EM reconstructions of Escherichia coli RNAP bound to NusG, or NusA, or both. RNAP conformational changes, referred to as swivelling, correlate with transcriptional pausing. NusA facilitates RNAP swivelling to further increase pausing, while NusG counteracts this role. Their structural effects are consistent with biochemical results on two categories of transcriptional pauses. In addition, the structures suggest a cooperative mechanism of NusA and NusG during Rho-mediated transcription termination. Our results provide a structural rationale for the stochastic nature of pausing and termination and how NusA and NusG can modulate it. Pausing of RNA polymerase (RNAP) and transcription is regulated by the NusA and NusG transcription factors in bacteria. Here the authors provide structural evidence for how they interact with RNAP to carry out their pausing roles and also reveal functions for NusA and NusG in transcription termination.
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Affiliation(s)
- Chengjin Zhu
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
| | - Xieyang Guo
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France.,GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, UK
| | - Philippe Dumas
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
| | - Maria Takacs
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
| | - Mo'men Abdelkareem
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
| | - Arnaud Vanden Broeck
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
| | - Charlotte Saint-André
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
| | - Gabor Papai
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
| | - Corinne Crucifix
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France
| | - Julio Ortiz
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France.,Forschungszentrum Jülich, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Jülich, Germany
| | - Albert Weixlbaumer
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404, Illkirch, France. .,Université de Strasbourg, 67404, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France.
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30
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Bailey EJ, Gottesman ME, Gonzalez RL. NusG-mediated Coupling of Transcription and Translation Enhances Gene Expression by Suppressing RNA Polymerase Backtracking. J Mol Biol 2022; 434:167330. [PMID: 34710399 PMCID: PMC9833396 DOI: 10.1016/j.jmb.2021.167330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/09/2021] [Accepted: 10/19/2021] [Indexed: 02/01/2023]
Abstract
In bacteria, transcription is coupled to, and can be regulated by, translation. Although recent structural studies suggest that the N-utilization substance G (NusG) transcription factor can serve as a direct, physical link between the transcribing RNA polymerase (RNAP) and the lead ribosome, mechanistic studies investigating the potential role of NusG in mediating transcription-translation coupling are lacking. Here, we report development of a cellular extract- and reporter gene-based, in vitro biochemical system that supports transcription-translation coupling as well as the use of this system to study the role of NusG in coupling. Our findings show that NusG is required for coupling and that the enhanced gene expression that results from coupling is dependent on the ability of NusG to directly interact with the lead ribosome. Moreover, we provide strong evidence that NusG-mediated coupling enhances gene expression through a mechanism in which the lead ribosome that is tethered to the RNAP by NusG suppresses spontaneous backtracking of the RNAP on its DNA template that would otherwise inhibit transcription.
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Affiliation(s)
- Elizabeth J. Bailey
- Department of Chemistry, Columbia University, 3000 Broadway, MC3126, New York, NY 10027, USA,Current Address: Center for Research on Learning and Teaching in Engineering, University of Michigan, 2609 Draper Drive, Ann Arbor, MI 48109, USA
| | - Max E. Gottesman
- Department of Microbiology and Immunology, Columbia University Medical Center, 701 West 168 Street, New York, NY 10032, USA,To whom correspondence should be addressed: Max E. Gottesman, Department of Microbiology and Immunology, Columbia University Medical Center, 701 West 168 Street, New York, NY 10032 USA Tel.: (212) 305-6900; Fax: (212) 305-1468; and Ruben L. Gonzalez, Jr., Department of Chemistry, Columbia University, 3000 Broadway, MC3126, New York, NY 10027, USA, Tel.: (212) 854-1096; Fax: (212) 932-1289;
| | - Ruben L. Gonzalez
- Department of Chemistry, Columbia University, 3000 Broadway, MC3126, New York, NY 10027, USA,To whom correspondence should be addressed: Max E. Gottesman, Department of Microbiology and Immunology, Columbia University Medical Center, 701 West 168 Street, New York, NY 10032 USA Tel.: (212) 305-6900; Fax: (212) 305-1468; and Ruben L. Gonzalez, Jr., Department of Chemistry, Columbia University, 3000 Broadway, MC3126, New York, NY 10027, USA, Tel.: (212) 854-1096; Fax: (212) 932-1289;
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31
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Dynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation. Proc Natl Acad Sci U S A 2021; 118:2109026118. [PMID: 34782462 DOI: 10.1073/pnas.2109026118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 11/18/2022] Open
Abstract
Cotranscriptional RNA folding is widely assumed to influence the timely control of gene expression, but our understanding remains limited. In bacteria, the fluoride (F-)-sensing riboswitch is a transcriptional control element essential to defend against toxic F- levels. Using this model riboswitch, we find that its ligand F- and essential bacterial transcription factor NusA compete to bind the cotranscriptionally folding RNA, opposing each other's modulation of downstream pausing and termination by RNA polymerase. Single-molecule fluorescence assays probing active transcription elongation complexes discover that NusA unexpectedly binds highly reversibly, frequently interrogating the complex for emerging, cotranscriptionally folding RNA duplexes. NusA thus fine-tunes the transcription rate in dependence of the ligand-responsive higher-order structure of the riboswitch. At the high NusA concentrations found intracellularly, this dynamic modulation is expected to lead to adaptive bacterial transcription regulation with fast response times.
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32
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Soffer A, Eisdorfer SA, Ifrach M, Ilic S, Afek A, Schussheim H, Vilenchik D, Akabayov B. Inferring primase-DNA specific recognition using a data driven approach. Nucleic Acids Res 2021; 49:11447-11458. [PMID: 34718733 PMCID: PMC8599759 DOI: 10.1093/nar/gkab956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 12/11/2022] Open
Abstract
DNA–protein interactions play essential roles in all living cells. Understanding of how features embedded in the DNA sequence affect specific interactions with proteins is both challenging and important, since it may contribute to finding the means to regulate metabolic pathways involving DNA–protein interactions. Using a massive experimental benchmark dataset of binding scores for DNA sequences and a machine learning workflow, we describe the binding to DNA of T7 primase, as a model system for specific DNA–protein interactions. Effective binding of T7 primase to its specific DNA recognition sequences triggers the formation of RNA primers that serve as Okazaki fragment start sites during DNA replication.
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Affiliation(s)
- Adam Soffer
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Data Science Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,School of Computer and Electrical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Sarah A Eisdorfer
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Morya Ifrach
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stefan Ilic
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ariel Afek
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Hallel Schussheim
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Dan Vilenchik
- Data Science Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,School of Computer and Electrical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Barak Akabayov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Data Science Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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33
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Abstract
To exert their functions, RNAs adopt diverse structures, ranging from simple secondary to complex tertiary and quaternary folds. In vivo, RNA folding starts with RNA transcription, and a wide variety of processes are coupled to co-transcriptional RNA folding events, including the regulation of fundamental transcription dynamics, gene regulation by mechanisms like attenuation, RNA processing or ribonucleoprotein particle formation. While co-transcriptional RNA folding and associated co-transcriptional processes are by now well accepted as pervasive regulatory principles in all organisms, investigations into the role of the transcription machinery in co-transcriptional folding processes have so far largely focused on effects of the order in which RNA regions are produced and of transcription kinetics. Recent structural and structure-guided functional analyses of bacterial transcription complexes increasingly point to an additional role of RNA polymerase and associated transcription factors in supporting co-transcriptional RNA folding by fostering or preventing strategic contacts to the nascent transcripts. In general, the results support the view that transcription complexes can act as RNA chaperones, a function that has been suggested over 30 years ago. Here, we discuss transcription complexes as RNA chaperones based on recent examples from bacterial transcription.
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Affiliation(s)
- Nelly Said
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany
| | - Markus C Wahl
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany.,Helmholtz-Zentrum Berlin Für Materialien Und Energie, Macromolecular Crystallography, Berlin, Germany
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34
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Webster MW, Weixlbaumer A. Macromolecular assemblies supporting transcription-translation coupling. Transcription 2021; 12:103-125. [PMID: 34570660 DOI: 10.1080/21541264.2021.1981713] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Coordination between the molecular machineries that synthesize and decode prokaryotic mRNAs is an important layer of gene expression control known as transcription-translation coupling. While it has long been known that translation can regulate transcription and vice-versa, recent structural and biochemical work has shed light on the underlying mechanistic basis. Complexes of RNA polymerase linked to a trailing ribosome (expressomes) have been structurally characterized in a variety of states at near-atomic resolution, and also directly visualized in cells. These data are complemented by recent biochemical and biophysical analyses of transcription-translation systems and the individual components within them. Here, we review our improved understanding of the molecular basis of transcription-translation coupling. These insights are discussed in relation to our evolving understanding of the role of coupling in cells.
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Affiliation(s)
- Michael W Webster
- Department of Integrated Structural Biology, Institut de Gé né tique et de Biologie Molé culaire et Cellulaire (IGBMC), Illkirch Cedex, France.,Université de Strasbourg, Strasbourg, France.,CNRS Umr 7104, Illkirch Cedex.,Inserm U1258, Illkirch Cedex, France
| | - Albert Weixlbaumer
- Department of Integrated Structural Biology, Institut de Gé né tique et de Biologie Molé culaire et Cellulaire (IGBMC), Illkirch Cedex, France.,Université de Strasbourg, Strasbourg, France.,CNRS Umr 7104, Illkirch Cedex.,Inserm U1258, Illkirch Cedex, France
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35
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Abstract
The low G + C Gram-positive bacteria represent some of the most medically and industrially important microorganisms. They are relied on for the production of food and dietary supplements, enzymes and antibiotics, as well as being responsible for the majority of nosocomial infections and serving as a reservoir for antibiotic resistance. Control of gene expression in this group is more highly studied than in any bacteria other than the Gram-negative model Escherichia coli, yet until recently no structural information on RNA polymerase (RNAP) from this group was available. This review will summarize recent reports on the high-resolution structure of RNAP from the model low G + C representative Bacillus subtilis, including the role of auxiliary subunits δ and ε, and outline approaches for the development of antimicrobials to target RNAP from this group.
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Affiliation(s)
- Michael Miller
- School Of Environmental And Life Sciences, University Of Newcastle, Callaghan, NSW, Australia
| | - Aaron J Oakley
- School Of Environmental And Life Sciences, University Of Newcastle, Callaghan, NSW, Australia
| | - Peter J Lewis
- School Of Environmental And Life Sciences, University Of Newcastle, Callaghan, NSW, Australia.,School Of Chemistry And Molecular Bioscience, University Of Wollongong And Illawarra Health And Medical Research Institute, Wollongong, Nsw, Australia
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36
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Abstract
Cellular life depends on transcription of DNA by RNA polymerase to express genetic information. RNA polymerase has evolved not just to read information from DNA and write it to RNA but also to sense and process information from the cellular and extracellular environments. Much of this information processing occurs during transcript elongation, when transcriptional pausing enables regulatory decisions. Transcriptional pauses halt RNA polymerase in response to DNA and RNA sequences and structures at locations and times that help coordinate interactions with small molecules and transcription factors important for regulation. Four classes of transcriptional pause signals are now evident after decades of study: elemental pauses, backtrack pauses, hairpin-stabilized pauses, and regulator-stabilized pauses. In this review, I describe current understanding of the molecular mechanisms of these four classes of pause signals, remaining questions about how RNA polymerase responds to pause signals, and the many exciting directions now open to understand pausing and the regulation of transcript elongation on a genome-wide scale. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Robert Landick
- Department of Biochemistry and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
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37
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Bergkessel M. Bacterial transcription during growth arrest. Transcription 2021; 12:232-249. [PMID: 34486930 PMCID: PMC8632087 DOI: 10.1080/21541264.2021.1968761] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/12/2022] Open
Abstract
Bacteria in most natural environments spend substantial periods of time limited for essential nutrients and not actively dividing. While transcriptional activity under these conditions is substantially reduced compared to that occurring during active growth, observations from diverse organisms and experimental approaches have shown that new transcription still occurs and is important for survival. Much of our understanding of transcription regulation has come from measuring transcripts in exponentially growing cells, or from in vitro experiments focused on transcription from highly active promoters by the housekeeping RNA polymerase holoenzyme. The fact that transcription during growth arrest occurs at low levels and is highly heterogeneous has posed challenges for its study. However, new methods of measuring low levels of gene expression activity, even in single cells, offer exciting opportunities for directly investigating transcriptional activity and its regulation during growth arrest. Furthermore, much of the rich structural and biochemical data from decades of work on the bacterial transcriptional machinery is also relevant to growth arrest. In this review, the physiological changes likely affecting transcription during growth arrest are first considered. Next, possible adaptations to help facilitate ongoing transcription during growth arrest are discussed. Finally, new insights from several recently published datasets investigating mRNA transcripts in single bacterial cells at various growth phases will be explored. Keywords: Growth arrest, stationary phase, RNA polymerase, nucleoid condensation, population heterogeneity.
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38
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Freddolino PL, Amemiya HM, Goss TJ, Tavazoie S. Dynamic landscape of protein occupancy across the Escherichia coli chromosome. PLoS Biol 2021; 19:e3001306. [PMID: 34170902 PMCID: PMC8282354 DOI: 10.1371/journal.pbio.3001306] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 07/15/2021] [Accepted: 06/02/2021] [Indexed: 12/18/2022] Open
Abstract
Free-living bacteria adapt to environmental change by reprogramming gene expression through precise interactions of hundreds of DNA-binding proteins. A predictive understanding of bacterial physiology requires us to globally monitor all such protein-DNA interactions across a range of environmental and genetic perturbations. Here, we show that such global observations are possible using an optimized version of in vivo protein occupancy display technology (in vivo protein occupancy display-high resolution, IPOD-HR) and present a pilot application to Escherichia coli. We observe that the E. coli protein-DNA interactome organizes into 2 distinct prototypic features: (1) highly dynamic condition-dependent transcription factor (TF) occupancy; and (2) robust kilobase scale occupancy by nucleoid factors, forming silencing domains analogous to eukaryotic heterochromatin. We show that occupancy dynamics across a range of conditions can rapidly reveal the global transcriptional regulatory organization of a bacterium. Beyond discovery of previously hidden regulatory logic, we show that these observations can be utilized to computationally determine sequence specificity models for the majority of active TFs. Our study demonstrates that global observations of protein occupancy combined with statistical inference can rapidly and systematically reveal the transcriptional regulatory and structural features of a bacterial genome. This capacity is particularly crucial for non-model bacteria that are not amenable to routine genetic manipulation.
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Affiliation(s)
- Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Haley M. Amemiya
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Thomas J. Goss
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Saeed Tavazoie
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
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39
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Understanding transcription across scales: From base pairs to chromosomes. Mol Cell 2021; 81:1601-1616. [PMID: 33770487 DOI: 10.1016/j.molcel.2021.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
The influence of genome organization on transcription is central to our understanding of cell type specification. Higher-order genome organization is established through short- and long-range DNA interactions. Coordination of these interactions, from single atoms to entire chromosomes, plays a fundamental role in transcriptional control of gene expression. Loss of this coupling can result in disease. Analysis of transcriptional regulation typically involves disparate experimental approaches, from structural studies that define angstrom-level interactions to cell-biological and genomic approaches that assess mesoscale relationships. Thus, to fully understand the mechanisms that regulate gene expression, it is critical to integrate the findings gained across these distinct size scales. In this review, I illustrate fundamental ways in which cells regulate transcription in the context of genome organization.
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40
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Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria. Nat Commun 2021; 12:906. [PMID: 33568644 PMCID: PMC7876045 DOI: 10.1038/s41467-021-21150-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 01/14/2021] [Indexed: 01/29/2023] Open
Abstract
Promoter-proximal pausing regulates eukaryotic gene expression and serves as checkpoints to assemble elongation/splicing machinery. Little is known how broadly this type of pausing regulates transcription in bacteria. We apply nascent elongating transcript sequencing combined with RNase I footprinting for genome-wide analysis of σ70-dependent transcription pauses in Escherichia coli. Retention of σ70 induces strong backtracked pauses at a 10−20-bp distance from many promoters. The pauses in the 10−15-bp register of the promoter are dictated by the canonical −10 element, 6−7 nt spacer and “YR+1Y” motif centered at the transcription start site. The promoters for the pauses in the 16−20-bp register contain an additional −10-like sequence recognized by σ70. Our in vitro analysis reveals that DNA scrunching is involved in these pauses relieved by Gre cleavage factors. The genes coding for transcription factors are enriched in these pauses, suggesting that σ70 and Gre proteins regulate transcription in response to changing environmental cues. Transcription by bacterial RNA polymerase is interrupted by pausing events that play diverse regulatory roles. Here, the authors find that a large number of E. coli sigma70-dependent pauses, clustered at a 10−20-bp distance from promoters, are regulated by Gre cleavage factors constituting a mechanism for rapid response to changing environmental cues.
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41
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Shi J, Wen A, Zhao M, Jin S, You L, Shi Y, Dong S, Hua X, Zhang Y, Feng Y. Structural basis of Mfd-dependent transcription termination. Nucleic Acids Res 2021; 48:11762-11772. [PMID: 33068413 PMCID: PMC7672476 DOI: 10.1093/nar/gkaa904] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/26/2020] [Accepted: 10/01/2020] [Indexed: 11/16/2022] Open
Abstract
Mfd-dependent transcription termination plays an important role in transcription-coupled DNA repair, transcription-replication conflict resolution, and antimicrobial resistance development. Despite extensive studies, the molecular mechanism of Mfd-dependent transcription termination in bacteria remains unclear, with several long-standing puzzles. How Mfd is activated by stalled RNA polymerase (RNAP) and how activated Mfd translocates along the DNA are unknown. Here, we report the single-particle cryo-electron microscopy structures of T. thermophilus Mfd-RNAP complex with and without ATPγS. The structures reveal that Mfd undergoes profound conformational changes upon activation, contacts the RNAP β1 domain and its clamp, and pries open the RNAP clamp. These structures provide a foundation for future studies aimed at dissecting the precise mechanism of Mfd-dependent transcription termination and pave the way for rational drug design targeting Mfd for the purpose of tackling the antimicrobial resistance crisis.
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Affiliation(s)
- Jing Shi
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China.,Department of Pathology, 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
| | - Aijia Wen
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Minxing Zhao
- Department of Emergency Medicine of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Sha Jin
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Linlin You
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Shi
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shuling Dong
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xiaoting Hua
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310058, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China.,Department of Pathology, 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
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42
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Irastortza-Olaziregi M, Amster-Choder O. Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises. Front Microbiol 2021; 11:624830. [PMID: 33552035 PMCID: PMC7858274 DOI: 10.3389/fmicb.2020.624830] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/18/2020] [Indexed: 01/17/2023] Open
Abstract
Coupled transcription-translation (CTT) is a hallmark of prokaryotic gene expression. CTT occurs when ribosomes associate with and initiate translation of mRNAs whose transcription has not yet concluded, therefore forming "RNAP.mRNA.ribosome" complexes. CTT is a well-documented phenomenon that is involved in important gene regulation processes, such as attenuation and operon polarity. Despite the progress in our understanding of the cellular signals that coordinate CTT, certain aspects of its molecular architecture remain controversial. Additionally, new information on the spatial segregation between the transcriptional and the translational machineries in certain species, and on the capability of certain mRNAs to localize translation-independently, questions the unanimous occurrence of CTT. Furthermore, studies where transcription and translation were artificially uncoupled showed that transcription elongation can proceed in a translation-independent manner. Here, we review studies supporting the occurrence of CTT and findings questioning its extent, as well as discuss mechanisms that may explain both coupling and uncoupling, e.g., chromosome relocation and the involvement of cis- or trans-acting elements, such as small RNAs and RNA-binding proteins. These mechanisms impact RNA localization, stability, and translation. Understanding the two options by which genes can be expressed and their consequences should shed light on a new layer of control of bacterial transcripts fate.
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Affiliation(s)
- Mikel Irastortza-Olaziregi
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
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43
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Wang B, Artsimovitch I. NusG, an Ancient Yet Rapidly Evolving Transcription Factor. Front Microbiol 2021; 11:619618. [PMID: 33488562 PMCID: PMC7819879 DOI: 10.3389/fmicb.2020.619618] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/07/2020] [Indexed: 12/19/2022] Open
Abstract
Timely and accurate RNA synthesis depends on accessory proteins that instruct RNA polymerase (RNAP) where and when to start and stop transcription. Among thousands of transcription factors, NusG/Spt5 stand out as the only universally conserved family of regulators. These proteins interact with RNAP to promote uninterrupted RNA synthesis and with diverse cellular partners to couple transcription to RNA processing, modification or translation, or to trigger premature termination of aberrant transcription. NusG homologs are present in all cells that utilize bacterial-type RNAP, from endosymbionts to plants, underscoring their ancient and essential function. Yet, in stark contrast to other core RNAP components, NusG family is actively evolving: horizontal gene transfer and sub-functionalization drive emergence of NusG paralogs, such as bacterial LoaP, RfaH, and UpxY. These specialized regulators activate a few (or just one) operons required for expression of antibiotics, capsules, secretion systems, toxins, and other niche-specific macromolecules. Despite their common origin and binding site on the RNAP, NusG homologs differ in their target selection, interacting partners and effects on RNA synthesis. Even among housekeeping NusGs from diverse bacteria, some factors promote pause-free transcription while others slow the RNAP down. Here, we discuss structure, function, and evolution of NusG proteins, focusing on unique mechanisms that determine their effects on gene expression and enable bacterial adaptation to diverse ecological niches.
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Affiliation(s)
- Bing Wang
- Department of Microbiology and the Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Irina Artsimovitch
- Department of Microbiology and the Center for RNA Biology, The Ohio State University, Columbus, OH, United States
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44
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Said N, Hilal T, Sunday ND, Khatri A, Bürger J, Mielke T, Belogurov GA, Loll B, Sen R, Artsimovitch I, Wahl MC. Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase ρ. Science 2021; 371:eabd1673. [PMID: 33243850 PMCID: PMC7864586 DOI: 10.1126/science.abd1673] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/26/2020] [Indexed: 12/31/2022]
Abstract
Factor-dependent transcription termination mechanisms are poorly understood. We determined a series of cryo-electron microscopy structures portraying the hexameric adenosine triphosphatase (ATPase) ρ on a pathway to terminating NusA/NusG-modified elongation complexes. An open ρ ring contacts NusA, NusG, and multiple regions of RNA polymerase, trapping and locally unwinding proximal upstream DNA. NusA wedges into the ρ ring, initially sequestering RNA. Upon deflection of distal upstream DNA over the RNA polymerase zinc-binding domain, NusA rotates underneath one capping ρ subunit, which subsequently captures RNA. After detachment of NusG and clamp opening, RNA polymerase loses its grip on the RNA:DNA hybrid and is inactivated. Our structural and functional analyses suggest that ρ, and other termination factors across life, may use analogous strategies to allosterically trap transcription complexes in a moribund state.
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Affiliation(s)
- Nelly Said
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Tarek Hilal
- Research Center of Electron Microscopy and Core Facility BioSupraMol, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Nicholas D Sunday
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Ajay Khatri
- Laboratory of Transcription, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Jörg Bürger
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
- Institute of Medical Physics und Biophysics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
| | | | - Bernhard Loll
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Ranjan Sen
- Laboratory of Transcription, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Irina Artsimovitch
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
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45
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Lippa AM, Gebhardt MJ, Dove SL. H-NS-like proteins in Pseudomonas aeruginosa coordinately silence intragenic transcription. Mol Microbiol 2020; 115:1138-1151. [PMID: 33245158 DOI: 10.1111/mmi.14656] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 01/22/2023]
Abstract
The H-NS-like proteins MvaT and MvaU act coordinately as global repressors in Pseudomonas aeruginosa by binding to AT-rich regions of the chromosome. Although cells can tolerate loss of either protein, identifying their combined regulatory effects has been challenging because the loss of both proteins is lethal due to induction of prophage Pf4 and subsequent superinfection of the cell. In other bacteria, H-NS promotes the cellular fitness by inhibiting intragenic transcription from AT-rich target regions, preventing them from sequestering RNA polymerase; however, it is not known whether MvaT and MvaU function similarly. Here, we utilize a parental strain that cannot be infected by Pf4 phage to define the collective MvaT and MvaU regulon and demonstrate that the combined loss of both MvaT and MvaU leads to increased intragenic transcription from loci directly controlled by these proteins. We further show that the loss of MvaT and MvaU leads to a striking redistribution of RNA polymerase containing σ70 to genomic regions vacated by these proteins. Our findings suggest that the ability of H-NS-like proteins to repress intragenic transcription is a universal function of these proteins and point to a second mechanism by which MvaT and MvaU may contribute to the growth of P. aeruginosa.
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Affiliation(s)
- Andrew M Lippa
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael J Gebhardt
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Simon L Dove
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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46
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Kim AK, Porter LL. Functional and Regulatory Roles of Fold-Switching Proteins. Structure 2020; 29:6-14. [PMID: 33176159 DOI: 10.1016/j.str.2020.10.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/15/2020] [Accepted: 10/20/2020] [Indexed: 01/08/2023]
Abstract
Fold-switching proteins respond to cellular stimuli by remodeling their secondary structures and changing their functions. Whereas several previous reviews have focused on various structural, physical-chemical, and evolutionary aspects of this newly emerging class of proteins, this minireview focuses on how fold switching modulates protein function and regulates biological processes. It first compares and contrasts fold switchers with other known types of proteins. Second, it presents examples of how various proteins can change their functions through fold switching. Third, it demonstrates that fold switchers can regulate biological processes by discussing two proteins, RfaH and KaiB, whose dramatic secondary structure remodeling events directly affect gene expression and a circadian clock, respectively. Finally, this minireview discusses how the field of protein fold switching might advance.
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Affiliation(s)
- Allen K Kim
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren L Porter
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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47
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Yakhnin AV, Kashlev M, Babitzke P. NusG-dependent RNA polymerase pausing is a frequent function of this universally conserved transcription elongation factor. Crit Rev Biochem Mol Biol 2020; 55:716-728. [PMID: 33003953 DOI: 10.1080/10409238.2020.1828261] [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] [Indexed: 10/23/2022]
Abstract
Although transcription by RNA polymerase (RNAP) is highly processive, elongation can be transiently halted by RNAP pausing. Pausing provides time for diverse regulatory events to occur such as RNA folding and regulatory factor binding. The transcription elongation factors NusA and NusG dramatically affect the frequency and duration of RNAP pausing, and hence regulation of transcription. NusG is the only transcription factor conserved in all three domains of life; its homolog in archaea and eukaryotes is Spt5. This review focuses on NusG-dependent pausing, which is a common occurrence in Bacillus subtilis. B. NusG induces pausing about once per 3 kb at a consensus TTNTTT motif in the non-template DNA strand within the paused transcription bubble. A conserved region of NusG contacts the TTNTTT motif to stabilize the paused transcription elongation complex (TEC) in multiple catalytically inactive RNAP conformations. The density of NusG-dependent pause sites is 3-fold higher in untranslated regions, suggesting that pausing could regulate the expression of hundreds of genes in B. subtilis. We describe how pausing in 5' leader regions contributes to regulating the expression of B. subtilis genes by transcription attenuation and translation control mechanisms. As opposed to the broadly accepted view that NusG is an anti-pausing factor, phylogenetic analyses suggest that NusG-dependent pausing is a widespread mechanism in bacteria. This function of NusG is consistent with the well-established role of its eukaryotic homolog Spt5 in promoter-proximal pausing. Since NusG is present in all domains of life, NusG-dependent pausing could be a conserved mechanism in all organisms.
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Affiliation(s)
- Alexander V Yakhnin
- NCI RNA Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA
| | - Mikhail Kashlev
- NCI RNA Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
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48
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O'Reilly FJ, Xue L, Graziadei A, Sinn L, Lenz S, Tegunov D, Blötz C, Singh N, Hagen WJH, Cramer P, Stülke J, Mahamid J, Rappsilber J. In-cell architecture of an actively transcribing-translating expressome. Science 2020; 369:554-557. [PMID: 32732422 DOI: 10.1126/science.abb3758] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/01/2020] [Indexed: 12/18/2022]
Abstract
Structural biology studies performed inside cells can capture molecular machines in action within their native context. In this work, we developed an integrative in-cell structural approach using the genome-reduced human pathogen Mycoplasma pneumoniae We combined whole-cell cross-linking mass spectrometry, cellular cryo-electron tomography, and integrative modeling to determine an in-cell architecture of a transcribing and translating expressome at subnanometer resolution. The expressome comprises RNA polymerase (RNAP), the ribosome, and the transcription elongation factors NusG and NusA. We pinpointed NusA at the interface between a NusG-bound elongating RNAP and the ribosome and propose that it can mediate transcription-translation coupling. Translation inhibition dissociated the expressome, whereas transcription inhibition stalled and rearranged it. Thus, the active expressome architecture requires both translation and transcription elongation within the cell.
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Affiliation(s)
- Francis J O'Reilly
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Liang Xue
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Andrea Graziadei
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Ludwig Sinn
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Swantje Lenz
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Dimitry Tegunov
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Cedric Blötz
- Department of General Microbiology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Neil Singh
- Department of General Microbiology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Wim J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany. .,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
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49
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Washburn RS, Zuber PK, Sun M, Hashem Y, Shen B, Li W, Harvey S, Acosta Reyes FJ, Gottesman ME, Knauer SH, Frank J. Escherichia coli NusG Links the Lead Ribosome with the Transcription Elongation Complex. iScience 2020; 23:101352. [PMID: 32726726 PMCID: PMC7390762 DOI: 10.1016/j.isci.2020.101352] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/04/2020] [Accepted: 07/03/2020] [Indexed: 02/07/2023] Open
Abstract
It has been known for more than 50 years that transcription and translation are physically coupled in bacteria, but whether or not this coupling may be mediated by the two-domain protein N-utilization substance (Nus) G in Escherichia coli is still heavily debated. Here, we combine integrative structural biology and functional analyses to provide conclusive evidence that NusG can physically link transcription with translation by contacting both RNA polymerase and the ribosome. We present a cryo-electron microscopy structure of a NusG:70S ribosome complex and nuclear magnetic resonance spectroscopy data revealing simultaneous binding of NusG to RNAP and the intact 70S ribosome, providing the first direct structural evidence for NusG-mediated coupling. Furthermore, in vivo reporter assays show that recruitment of NusG occurs late in transcription and strongly depends on translation. Thus, our data suggest that coupling occurs initially via direct RNAP:ribosome contacts and is then mediated by NusG.
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Affiliation(s)
- Robert S Washburn
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Philipp K Zuber
- Biochemistry IV - Biopolymers, University of Bayreuth, 95447 Bayreuth, Germany
| | - Ming Sun
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Yaser Hashem
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Bingxin Shen
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Wen Li
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Sho Harvey
- University of Michigan, Ann Arbor, MI 48109, USA
| | - Francisco J Acosta Reyes
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Max E Gottesman
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA.
| | - Stefan H Knauer
- Biochemistry IV - Biopolymers, University of Bayreuth, 95447 Bayreuth, Germany.
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA.
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50
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Kim S, Beltran B, Irnov I, Jacobs-Wagner C. Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling. Cell 2020; 179:106-119.e16. [PMID: 31539491 DOI: 10.1016/j.cell.2019.08.033] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 06/14/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022]
Abstract
Genes are often transcribed by multiple RNA polymerases (RNAPs) at densities that can vary widely across genes and environmental conditions. Here, we provide in vitro and in vivo evidence for a built-in mechanism by which co-transcribing RNAPs display either collaborative or antagonistic dynamics over long distances (>2 kb) through transcription-induced DNA supercoiling. In Escherichia coli, when the promoter is active, co-transcribing RNAPs translocate faster than a single RNAP, but their average speed is not altered by large variations in promoter strength and thus RNAP density. Environmentally induced promoter repression reduces the elongation efficiency of already-loaded RNAPs, causing premature termination and quick synthesis arrest of no-longer-needed proteins. This negative effect appears independent of RNAP convoy formation and is abrogated by topoisomerase I activity. Antagonistic dynamics can also occur between RNAPs from divergently transcribed gene pairs. Our findings may be broadly applicable given that transcription on topologically constrained DNA is the norm across organisms.
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Affiliation(s)
- Sangjin Kim
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA.
| | - Bruno Beltran
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA
| | - Irnov Irnov
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA.
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