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He C, He G, Feng Y. Structural basis of phage transcriptional regulation. Structure 2024; 32:1031-1039. [PMID: 39067444 DOI: 10.1016/j.str.2024.07.002] [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: 04/24/2024] [Revised: 06/03/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024]
Abstract
Phages are the most prevalent and diverse entities in the biosphere and represent the simplest systems that are capable of self-replication. Many fundamental concepts of transcriptional regulation were revealed through phage studies. The replication of phages within bacteria entails the hijacking of the host transcription machinery. Typically, this is accomplished through proteins and RNAs encoded by the phage genome that bind to the host RNA polymerase and modify its characteristics. Understanding these processes offers valuable insights into the mechanisms of bacterial transcription itself. Historically, X-ray crystallography has been the major tool for elucidating the structural basis of phage transcriptional regulation. In recent years, the application of cryoelectron microscopy has not only allowed the exploration of protein-protein and protein-nucleic acid interactions at near-atomic resolution but also captured transient intermediate states, further expanding our mechanistic understanding of phage transcriptional regulation.
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Affiliation(s)
- Chuchu He
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guanchen He
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Key Laboratory for Diagnosis and Treatment of Physic-Chemical and Aging Injury Diseases of Zhejiang Province, Hangzhou 310003, China.
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Bao Y, Cao X, Landick R. RNA polymerase SI3 domain modulates global transcriptional pausing and pause-site fluctuations. Nucleic Acids Res 2024; 52:4556-4574. [PMID: 38554114 PMCID: PMC11077087 DOI: 10.1093/nar/gkae209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 03/03/2024] [Accepted: 03/26/2024] [Indexed: 04/01/2024] Open
Abstract
Transcriptional pausing aids gene regulation by cellular RNA polymerases (RNAPs). A surface-exposed domain inserted into the catalytic trigger loop (TL) of Escherichia coli RNAP, called SI3, modulates pausing and is essential for growth. Here we describe a viable E. coli strain lacking SI3 enabled by a suppressor TL substitution (β'Ala941→Thr; ΔSI3*). ΔSI3* increased transcription rate in vitro relative to ΔSI3, possibly explaining its viability, but retained both positive and negative effects of ΔSI3 on pausing. ΔSI3* inhibited pauses stabilized by nascent RNA structures (pause hairpins; PHs) but enhanced other pauses. Using NET-seq, we found that ΔSI3*-enhanced pauses resemble the consensus elemental pause sequence whereas sequences at ΔSI3*-suppressed pauses, which exhibited greater association with PHs, were more divergent. ΔSI3*-suppressed pauses also were associated with apparent pausing one nucleotide upstream from the consensus sequence, often generating tandem pause sites. These '-2 pauses' were stimulated by pyrophosphate in vitro and by addition of apyrase to degrade residual NTPs during NET-seq sample processing. We propose that some pauses are readily reversible by pyrophosphorolysis or single-nucleotide cleavage. Our results document multiple ways that SI3 modulates pausing in vivo and may explain discrepancies in consensus pause sequences in some NET-seq studies.
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Affiliation(s)
- Yu Bao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xinyun Cao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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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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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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King RA, Babbs M, Baugh K, Hamilton C. Isolation and Characterization of Phages That Bypass the Requirement for RNA-Mediated Antitermination. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:82-89. [PMID: 37350996 PMCID: PMC10282786 DOI: 10.1089/phage.2023.0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
Introduction The rpoCY75N mutation in the zinc-binding domain of the β' subunit of Escherichia coli RNA polymerase blocks the RNA-based mechanism of transcription antitermination utilized by bacteriophage HK022. Materials and Methods Mutant phages that overcome the block imposed by the rpoCY75N mutation are described. These phages, designated "orc" (overcomes rpoC), carry mutations that create new promoters. Promoter activity was assessed by cloning the respective regions from the wild-type and orc phages into a promoterless lacZ reporter vector. Results Reporter assays showed that the sequence originating from orc phages had significant promoter activity when compared with the equivalent sequence cloned from the parental phage. Conclusions The newly created promoters facilitate the expression of phage genes that are essential for growth on the rpoCY75N strain by bypassing transcription terminators. The small plaque phenotype of orc phages, when grown on the mutant host, suggests that suppression of the rpoCY75N mutation is incomplete.
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Affiliation(s)
- Rodney A. King
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, USA
| | - Millicent Babbs
- Owensboro Family Medicine, University of Louisville, Owensboro, Kentucky, USA
| | - Kimberly Baugh
- Department of Pharmacy, Franciscan Health Lafayette East, Lafayette, Indiana, USA
| | - Courtney Hamilton
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Kang JY, Mishanina TV, Bao Y, Chen J, Llewellyn E, Liu J, Darst SA, Landick R. An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options. Proc Natl Acad Sci U S A 2023; 120:e2215945120. [PMID: 36795753 PMCID: PMC9974457 DOI: 10.1073/pnas.2215945120] [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: 09/19/2022] [Accepted: 01/10/2023] [Indexed: 02/17/2023] Open
Abstract
Transcriptional pausing underpins the regulation of cellular RNA synthesis, but its mechanism remains incompletely understood. Sequence-specific interactions of DNA and RNA with the dynamic, multidomain RNA polymerase (RNAP) trigger reversible conformational changes at pause sites that temporarily interrupt the nucleotide addition cycle. These interactions initially rearrange the elongation complex (EC) into an elemental paused EC (ePEC). ePECs can form longer-lived PECs by further rearrangements or interactions of diffusible regulators. For both bacterial and mammalian RNAPs, a half-translocated state in which the next DNA template base fails to load into the active site appears central to the ePEC. Some RNAPs also swivel interconnected modules that may stabilize the ePEC. However, it is unclear whether swiveling and half-translocation are requisite features of a single ePEC state or if multiple ePEC states exist. Here, we use cryo-electron microscopy (cryo-EM) analysis of ePECs with different RNA-DNA sequences combined with biochemical probes of ePEC structure to define an interconverting ensemble of ePEC states. ePECs occupy either pre- or half-translocated states but do not always swivel, indicating that difficulty in forming the posttranslocated state at certain RNA-DNA sequences may be the essence of the ePEC. The existence of multiple ePEC conformations has broad implications for transcriptional regulation.
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Affiliation(s)
- Jin Young Kang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea
| | - Tatiana V. Mishanina
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Yu Bao
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI53706
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Eliza Llewellyn
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - James Liu
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI53706
| | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI53706
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI53706
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Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-André C, Weixlbaumer A. Structural insights into RNA-mediated transcription regulation in bacteria. Mol Cell 2022; 82:3885-3900.e10. [DOI: 10.1016/j.molcel.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/07/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
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