1
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Yin Z, Bird JG, Kaelber JT, Nickels BE, Ebright RH. In transcription antitermination by Qλ, NusA induces refolding of Qλ to form a nozzle that extends the RNA polymerase RNA-exit channel. Proc Natl Acad Sci U S A 2022; 119:e2205278119. [PMID: 35951650 PMCID: PMC9388147 DOI: 10.1073/pnas.2205278119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/08/2022] [Indexed: 01/24/2023] Open
Abstract
Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element to yield a Q-loading complex, and they translocate with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. In previous work, we showed that the Q protein of bacteriophage 21 (Q21) functions by forming a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of pause and termination RNA hairpins. Here, we report atomic structures of four states on the pathway of antitermination by the Q protein of bacteriophage λ (Qλ), a Q protein that shows no sequence similarity to Q21 and that, unlike Q21, requires the transcription elongation factor NusA for efficient antipausing and antitermination. We report structures of Qλ, the Qλ-QBE complex, the NusA-free pre-engaged Qλ-loading complex, and the NusA-containing engaged Qλ-loading complex. The results show that Qλ, like Q21, forms a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of RNA hairpins. However, the results show that Qλ has no three-dimensional structural similarity to Q21, employs a different mechanism of QBE recognition than Q21, and employs a more complex process for loading onto RNAP than Q21, involving recruitment of Qλ to form a pre-engaged loading complex, followed by NusA-facilitated refolding of Qλ to form an engaged loading complex. The results establish that Qλ and Q21 are not structural homologs and are solely functional analogs.
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Affiliation(s)
- Zhou Yin
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Jeremy G. Bird
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
| | - Jason T. Kaelber
- Rutgers Cryo-EM and Nanoimaging Facility, Rutgers University, Piscataway, NJ 08854
| | - Bryce E. Nickels
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
| | - Richard H. Ebright
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
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2
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Wen A, Zhao M, Jin S, Lu YQ, Feng Y. Structural basis of AlpA-dependent transcription antitermination. Nucleic Acids Res 2022; 50:8321-8330. [PMID: 35871295 PMCID: PMC9371919 DOI: 10.1093/nar/gkac608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 06/27/2022] [Accepted: 07/19/2022] [Indexed: 11/12/2022] Open
Abstract
AlpA positively regulates a programmed cell death pathway linked to the virulence of Pseudomonas aeruginosa by recognizing an AlpA binding element within the promoter, then binding RNA polymerase directly and allowing it to bypass an intrinsic terminator positioned downstream. Here, we report the single-particle cryo-electron microscopy structures of both an AlpA-loading complex and an AlpA-loaded complex. These structures indicate that the C-terminal helix-turn-helix motif of AlpA binds to the AlpA binding element and that the N-terminal segment of AlpA forms a narrow ring inside the RNA exit channel. AlpA was also revealed to render RNAP resistant to termination signals by prohibiting RNA hairpin formation in the RNA exit channel. Structural analysis predicted that AlpA, 21Q, λQ and 82Q share the same mechanism of transcription antitermination.
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Affiliation(s)
- Aijia Wen
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, 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, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine , Hangzhou 310058, China
| | - Yuan-Qiang Lu
- Department of Emergency Medicine of the First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 310003, China
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine , Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Immunity and Inflammatory diseases , Hangzhou 310058, China
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3
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NusA directly interacts with antitermination factor Q from phage λ. Sci Rep 2020; 10:6607. [PMID: 32313022 PMCID: PMC7171158 DOI: 10.1038/s41598-020-63523-5] [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: 11/20/2019] [Accepted: 03/27/2020] [Indexed: 12/03/2022] Open
Abstract
Antitermination (AT) is a ubiquitous principle in the regulation of bacterial transcription to suppress termination signals. In phage λ antiterminator protein Q controls the expression of the phage’s late genes with loading of λQ onto the transcription elongation complex halted at a σ-dependent pause requiring a specific DNA element. The molecular basis of λQ-dependent AT and its dependence on N-utilization substance (Nus) A is so far only poorly understood. Here we used solution-state nuclear magnetic resonance spectroscopy to show that the solution structure of λQ is in agreement with the crystal structure of an N-terminally truncated variant and that the 60 residues at the N-terminus are unstructured. We also provide evidence that multidomain protein NusA interacts directly with λQ via its N-terminal domain (NTD) and the acidic repeat (AR) 2 domain, with the λQ:NusA-AR2 interaction being able to release NusA autoinhibition. The binding sites for NusA-NTD and NusA-AR2 on λQ overlap and the interactions are mutually exclusive with similar affinities, suggesting distinct roles during λQ-dependent AT, e.g. the λQ:NusA-NTD interaction might position NusA-NTD in a way to suppress termination, making NusA-NTD repositioning a general scheme in AT mechanisms.
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4
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Structural basis of Q-dependent transcription antitermination. Nat Commun 2019; 10:2925. [PMID: 31266960 PMCID: PMC6606751 DOI: 10.1038/s41467-019-10958-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/12/2019] [Indexed: 01/25/2023] Open
Abstract
Bacteriophage Q protein engages σ-dependent paused RNA polymerase (RNAP) by binding to a DNA site embedded in late gene promoter and renders RNAP resistant to termination signals. Here, we report a single-particle cryo-electron microscopy (cryo-EM) structure of an intact Q-engaged arrested complex. The structure reveals key interactions responsible for σ-dependent pause, Q engagement, and Q-mediated transcription antitermination. The structure shows that two Q protomers (QI and QII) bind to a direct-repeat DNA site and contact distinct elements of the RNA exit channel. Notably, QI forms a narrow ring inside the RNA exit channel and renders RNAP resistant to termination signals by prohibiting RNA hairpin formation in the RNA exit channel. Because the RNA exit channel is conserved among all multisubunit RNAPs, it is likely to serve as an important contact site for regulators that modify the elongation properties of RNAP in other organisms, as well. Bacteriophage Q protein serves as a model regulator for the study of transcription elongation. Here the authors report a cryo-EM structure of an intact Q-engaged arrested complex, revealing the interactions responsible for σ-dependent pause, Q engagement, and Q-mediated transcription antitermination.
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5
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Leuzzi A, Grossi M, Di Martino ML, Pasqua M, Micheli G, Colonna B, Prosseda G. Role of the SRRz/Rz 1 lambdoid lysis cassette in the pathoadaptive evolution of Shigella. Int J Med Microbiol 2017; 307:268-275. [PMID: 28389211 DOI: 10.1016/j.ijmm.2017.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/21/2017] [Accepted: 03/27/2017] [Indexed: 12/25/2022] Open
Abstract
Shigella, the etiological agent of bacillary dysentery (shigellosis), is a highly adapted human pathogen. It evolved from an innocuous ancestor resembling the Escherichia coli strain by gain and loss of genes and functions. While the gain process concerns the acquisition of the genetic determinants of virulence, the loss is related to the adaptation of the genome to the new pathogenic status and occurs by pathoadaptive mutation of antivirulence genes. In this study, we highlight that the SRRz/Rz1 lambdoid lysis cassette, even though stably adopted in E. coli K12 by virtue of its beneficial effect on cell physiology, has undergone a significant decay in Shigella. Moreover, we show the antivirulence nature of the SRRz/Rz1 lysis cassette in Shigella. In fact, by restoring the SRRz/Rz1 expression in this pathogen, we observe an increased release of peptidoglycan fragments, causing an unbalance in the fine control exerted by Shigella on host innate immunity and a mitigation of its virulence. This strongly affects the virulence of Shigella and allows to consider the loss of SRRz/Rz1 lysis cassette as another pathoadaptive event in the life of Shigella.
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Affiliation(s)
- Adriano Leuzzi
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - Milena Grossi
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - Maria Letizia Di Martino
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - Martina Pasqua
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - Gioacchino Micheli
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Bianca Colonna
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - Gianni Prosseda
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy.
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6
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Rueggeberg KG, Toba FA, Bird JG, Franck N, Thompson MG, Hay AG. The lysis cassette of DLP12 defective prophage is regulated by RpoE. MICROBIOLOGY-SGM 2015; 161:1683-1693. [PMID: 25998262 DOI: 10.1099/mic.0.000115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Expression of the lysis cassette (essD, ybcT, rzpD/rzoD) from the defective lambdoid prophage at the 12th minute of Escherichia coli's genome (DLP12) is required in some strains for proper curli expression and biofilm formation. Regulating production of the lytic enzymes encoded by these genes is critical for maintaining cell wall integrity. In lambdoid phages, late-gene regulation is mediated by the vegetative sigma factor RpoD and the lambda antiterminator Qλ. We previously demonstrated that DLP12 contains a Q-like protein (QDLP12) that positively regulates transcription of the lysis cassette, but the sigma factor responsible for this transcription initiation remained to be elucidated. In silico analysis of essDp revealed the presence of a putative - 35 and - 10 sigma site recognized by the extracytoplasmic stress response sigma factor, RpoE. In this work, we report that RpoE overexpression promoted transcription from essDp in vivo, and in vitro using purified RNAP. We demonstrate that the - 35 region is important for RpoE binding in vitro and that this region is also important for QDLP12-mediated transcription of essDp in vivo. A bacterial two-hybrid assay indicated that QDLP12 and RpoE physically interact in vivo, consistent with what is seen for Qλ and RpoD. We propose that RpoE regulates transcription of the DLP12 lysis genes through interaction with QDLP12 and that proper expression is dependent on an intact - 35 sigma region in essDp. This work provides evidence that the unique Q-dependent regulatory mechanism of lambdoid phages has been co-opted by E. coli harbouring defective DLP12 and has been integrated into the tightly controlled RpoE regulon.
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Affiliation(s)
| | - Faustino A Toba
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Jeremy G Bird
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Nathan Franck
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | | | - Anthony G Hay
- Graduate Program in Environmental Toxicology, Cornell University, Ithaca, NY 14853, USA.,Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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7
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Strobel EJ, Roberts JW. Regulation of promoter-proximal transcription elongation: enhanced DNA scrunching drives λQ antiterminator-dependent escape from a σ70-dependent pause. Nucleic Acids Res 2014; 42:5097-108. [PMID: 24550164 PMCID: PMC4005639 DOI: 10.1093/nar/gku147] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
During initial transcription, RNA polymerase remains bound at the promoter and synthesizes RNA without movement along the DNA template, drawing downstream DNA into itself in a process called scrunching and thereby storing energy to sever the bonds that hold the enzyme at the promoter. We show that DNA scrunching also is the driving force behind the escape of RNA polymerase from a regulatory pause of the late gene operon of bacteriophage λ, and that this process is enhanced by the activity of the Q(λ) antiterminator. Furthermore, we show that failure of transcription complexes to escape the pause results in backtracking and arrest in a process analogous to abortive initiation. We identify a sequence element that modulates both abortive synthesis and the formation of arrested elongation complexes.
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Affiliation(s)
- Eric J Strobel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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8
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Vorobiev SM, Gensler Y, Vahedian-Movahed H, Seetharaman J, Su M, Huang JY, Xiao R, Kornhaber G, Montelione GT, Tong L, Ebright RH, Nickels BE. Structure of the DNA-binding and RNA-polymerase-binding region of transcription antitermination factor λQ. Structure 2014; 22:488-95. [PMID: 24440517 DOI: 10.1016/j.str.2013.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 12/18/2013] [Accepted: 12/20/2013] [Indexed: 10/25/2022]
Abstract
The bacteriophage λ Q protein is a transcription antitermination factor that controls expression of the phage late genes as a stable component of the transcription elongation complex. To join the elongation complex, λQ binds a specific DNA sequence element and interacts with RNA polymerase that is paused during early elongation. λQ binds to the paused early-elongation complex through interactions between λQ and two regions of RNA polymerase: region 4 of the σ(70) subunit and the flap region of the β subunit. We present the 2.1 Å resolution crystal structure of a portion of λQ containing determinants for interaction with DNA, interaction with region 4 of σ(70), and interaction with the β flap. The structure provides a framework for interpreting prior genetic and biochemical analysis and sets the stage for future structural studies to elucidate the mechanism by which λQ alters the functional properties of the transcription elongation complex.
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Affiliation(s)
- Sergey M Vorobiev
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
| | - Yocheved Gensler
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Hanif Vahedian-Movahed
- Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Jayaraman Seetharaman
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
| | - Min Su
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
| | - Janet Y Huang
- Center for Advanced Biotechnology and Medicine, Rutgers University, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers University, Piscataway, NJ 08854, USA
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Rutgers University, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers University, Piscataway, NJ 08854, USA
| | - Gregory Kornhaber
- Center for Advanced Biotechnology and Medicine, Rutgers University, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers University, Piscataway, NJ 08854, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Rutgers University, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers University, Piscataway, NJ 08854, USA
| | - Liang Tong
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
| | - Richard H Ebright
- Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
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9
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Rueggeberg KG, Toba FA, Thompson MG, Campbell BR, Hay AG. A Q-like transcription factor regulates biofilm development in Escherichia coli by controlling expression of the DLP12 lysis cassette. Microbiology (Reading) 2013; 159:691-700. [DOI: 10.1099/mic.0.064741-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Faustino A. Toba
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | | | - Bryan R. Campbell
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Anthony G. Hay
- Institute for Comparative and Environmental Toxicology, Cornell University, Ithaca, NY 14853, USA
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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10
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Abstract
For many bacteriophages (phages), the proteins responsible for host lysis and virion morphogenesis are expressed from the same polycistronic transcript. Such an expression pattern can potentially have a pleiotropic effect on the assembly rate and lysis time, thus affecting phage fitness. To study the effects of late promoter activity on phage life history traits and fitness, we constructed a series of isogenic phage lambda strains that differ only in their late promoter pR' sequences. The resulting late promoter activities ranged from 6 to 100% of the wild type's. The lysis times, burst sizes, and relative fitness were empirically determined for these strains. Our results showed that the lysis time is more sensitive than the assembly rate to variation in pR' activity. However, except for the strain with the lowest activity, the relative fitnesses of all the other strains are not significantly different from each other. Ad hoc models describing the effects of the late promoter activity on lysis time and assembly rate were constructed. The expected phage burst size and fitness curve were predicted from these models. Evolution of the late promoter activity was discussed in the context of phage life history trait evolution.
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11
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The bacteriophage lambda Q antiterminator protein contacts the beta-flap domain of RNA polymerase. Proc Natl Acad Sci U S A 2008; 105:15305-10. [PMID: 18832144 DOI: 10.1073/pnas.0805757105] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The multisubunit RNA polymerase (RNAP) in bacteria consists of a catalytically active core enzyme (alpha(2)beta beta'omega) complexed with a sigma factor that is required for promoter-specific transcription initiation. During early elongation the stability of interactions between sigma and core decreases, in part because of the nascent RNA-mediated destabilization of an interaction between region 4 of sigma and the flap domain of the beta-subunit (beta-flap). The nascent RNA-mediated destabilization of the sigma region 4/beta-flap interaction is required for the bacteriophage lambda Q antiterminator protein (lambdaQ) to engage the RNAP holoenzyme. Here, we provide an explanation for this requirement by showing that lambdaQ establishes direct contact with the beta-flap during the engagement process, thus competing with sigma(70) region 4 for access to the beta-flap. We also show that lambdaQ's affinity for the beta-flap is calibrated to ensure that lambdaQ activity is restricted to the lambda late promoter P(R'). Specifically, we find that strengthening the lambdaQ/beta-flap interaction allows lambdaQ to bypass the requirement for specific cis-acting sequence elements, a lambdaQ-DNA binding site and a RNAP pause-inducing element, that normally ensure lambdaQ is recruited exclusively to transcription complexes associated with P(R'). Our findings demonstrate that the beta-flap can serve as a direct target for regulators of elongation.
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12
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Nickels BE, Roberts CW, Roberts JW, Hochschild A. RNA-mediated destabilization of the sigma(70) region 4/beta flap interaction facilitates engagement of RNA polymerase by the Q antiterminator. Mol Cell 2006; 24:457-68. [PMID: 17081994 PMCID: PMC1797609 DOI: 10.1016/j.molcel.2006.09.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 07/31/2006] [Accepted: 09/11/2006] [Indexed: 10/24/2022]
Abstract
The bacterial RNA polymerase (RNAP) holoenzyme consists of a catalytic core enzyme (alpha(2)betabeta'omega) complexed with a sigma factor that is required for promoter-specific transcription initiation. During early elongation, the stability of interactions between sigma(70) (the primary sigma factor in Escherichia coli) and core decreases due to an ordered displacement of segments of sigma(70) from core triggered by growth of the nascent RNA. Here we demonstrate that the nascent RNA-mediated destabilization of an interaction between sigma(70) region 4 and the flap domain of the beta subunit is required for the bacteriophage lambda Q antiterminator protein to contact holoenzyme during early elongation. We demonstrate further that the requirement for nascent RNA in the process by which Q engages RNAP can be bypassed if sigma(70) region 4 is removed. Our findings illustrate how a regulator can exploit the nascent RNA-mediated reconfiguration of the holoenzyme to gain access to the enzyme during early elongation.
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Affiliation(s)
- Bryce E. Nickels
- Department of Microbiology and Molecular Genetics Harvard Medical School 200 Longwood Avenue Boston, MA 02115 Phone: (617) 432-1986 FAX: (617) 738-7664
| | - Christine W. Roberts
- Department of Molecular Biology & Genetics 349 Biotechnology Bldg. Cornell University Ithaca, New York 14853 Phone: (607) 255-2430 FAX: (607) 255-2428
| | - Jeffrey W. Roberts
- Department of Molecular Biology & Genetics 349 Biotechnology Bldg. Cornell University Ithaca, New York 14853 Phone: (607) 255-2430 FAX: (607) 255-2428
| | - Ann Hochschild
- Department of Microbiology and Molecular Genetics Harvard Medical School 200 Longwood Avenue Boston, MA 02115 Phone: (617) 432-1986 FAX: (617) 738-7664
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13
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Waldor MK, Friedman DI. Phage regulatory circuits and virulence gene expression. Curr Opin Microbiol 2005; 8:459-65. [PMID: 15979389 DOI: 10.1016/j.mib.2005.06.001] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Accepted: 06/09/2005] [Indexed: 11/19/2022]
Abstract
In many pathogenic bacteria, genes that encode virulence factors are located in the genomes of prophages. Clearly bacteriophages are important vectors for disseminating virulence genes, but, in addition, do phage regulatory circuits contribute to expression of these genes? Phages of the lambda family that have genes encoding Shiga toxin are found in certain pathogenic Escherichia coli (known as Shiga toxin producing E. coli) and the filamentous phage CTXphi, that carries genes encoding cholera toxin (CTX), is found in Vibrio cholerae. Both the lambda and CTXphi phages have repressor systems that maintain their respective prophages in a quiescent state, and in both types of prophages this repressed state is abolished when the host cell SOS response is activated. In the lambda type of prophages, only binding of the phage-encoded repressor is involved in repression and this repressor ultimately controls Shiga toxin production and/or release. In the CTXphi prophage, binding of LexA, the bacterial regulator of SOS, in addition to binding of the repressor is involved in repression; the repressor has only limited control over CTX production and has no influence on its release.
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Affiliation(s)
- Matthew K Waldor
- Department of Microbiology, Tufts University School of Medicine and Howard Hughes Medical Institute, Boston, MA 02111, USA
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14
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Abstract
The contribution of bacteriophage lambda to gene control research is far from over. A revised model of the lambda genetic switch includes extra cooperativity through octamerization of the cI repressor protein, mediated by long-range DNA looping. Structural analysis reveals remarkably subtle transcriptional activation by cI. The action of cI, activation by cII, and aspects of antitermination by N and Q all confirm the utility and versatility of simple, weak adhesive interactions mediated by nucleic acid tethers. New genetic and quantitative analysis of the lambda gene network is challenging cherished ideas about how complex behaviours emerge from this regulatory system.
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Affiliation(s)
- Ian B Dodd
- Discipline of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, South Australia 5005, Australia.
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