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Yao G, Le T, Korn AM, Peterson HN, Liu M, Gonzalez CF, Gill JJ. Phage Milagro: a platform for engineering a broad host range virulent phage for Burkholderia. J Virol 2023; 97:e0085023. [PMID: 37943040 PMCID: PMC10688314 DOI: 10.1128/jvi.00850-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/21/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Burkholderia infections are a significant concern in people with CF and other immunocompromising disorders, and are difficult to treat with conventional antibiotics due to their inherent drug resistance. Bacteriophages, or bacterial viruses, are now seen as a potential alternative therapy for these infections, but most of the naturally occurring phages are temperate and have narrow host ranges, which limit their utility as therapeutics. Here we describe the temperate Burkholderia phage Milagro and our efforts to engineer this phage into a potential therapeutic by expanding the phage host range and selecting for phage mutants that are strictly virulent. This approach may be used to generate new therapeutic agents for treating intractable infections in CF patients.
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Affiliation(s)
- Guichun Yao
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Tram Le
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Abby M. Korn
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Hannah N. Peterson
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Mei Liu
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Carlos F. Gonzalez
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Jason J. Gill
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
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2
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Hao N, Donnelly AJ, Dodd IB, Shearwin KE. When push comes to shove - RNA polymerase and DNA-bound protein roadblocks. Biophys Rev 2023; 15:355-366. [PMID: 37396453 PMCID: PMC10310618 DOI: 10.1007/s12551-023-01064-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/21/2023] [Indexed: 07/04/2023] Open
Abstract
In recent years, transcriptional roadblocking has emerged as a crucial regulatory mechanism in gene expression, whereby other DNA-bound obstacles can block the progression of transcribing RNA polymerase (RNAP), leading to RNAP pausing and ultimately dissociation from the DNA template. In this review, we discuss the mechanisms by which transcriptional roadblocks can impede RNAP progression, as well as how RNAP can overcome these obstacles to continue transcription. We examine different DNA-binding proteins involved in transcriptional roadblocking and their biophysical properties that determine their effectiveness in blocking RNAP progression. The catalytically dead CRISPR-Cas (dCas) protein is used as an example of an engineered programmable roadblock, and the current literature in understanding the polarity of dCas roadblocking is also discussed. Finally, we delve into a stochastic model of transcriptional roadblocking and highlight the importance of transcription factor binding kinetics and its resistance to dislodgement by an elongating RNAP in determining the strength of a roadblock.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Alana J. Donnelly
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Ian B. Dodd
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Keith E. Shearwin
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
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3
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Lu Y, Voros Z, Borjas G, Hendrickson C, Shearwin K, Dunlap D, Finzi L. RNA polymerase efficiently transcribes DNA-scaffolded, cooperative bacteriophage repressor complexes. FEBS Lett 2022; 596:1994-2006. [PMID: 35819073 PMCID: PMC9491066 DOI: 10.1002/1873-3468.14447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 11/07/2022]
Abstract
DNA can act as a scaffold for the cooperative binding of protein oligomers. For example, the phage 186 CI repressor forms a wheel of seven dimers wrapped in DNA with specific binding sites, while phage λ CI repressor dimers bind to two well-separated sets of operators, forming a DNA loop. Atomic force microscopy was used to measure transcription elongation by E. coli RNA polymerase through these protein complexes. 186 CI, or λ CI, bound along unlooped DNA negligibly interfered with transcription by RNAP. Wrapped and looped topologies induced by these scaffolded, cooperatively bound repressor oligomers did not form significantly better roadblocks to transcription. Thus, despite binding with high affinity, these repressors are not effective roadblocks to transcription.
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Affiliation(s)
- Yue Lu
- Physics Department, Emory University, Atlanta, GA, USA
| | | | | | | | - Keith Shearwin
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia
| | - David Dunlap
- Physics Department, Emory University, Atlanta, GA, USA
| | - Laura Finzi
- Physics Department, Emory University, Atlanta, GA, USA
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Sánchez-Osuna M, Cortés P, Lee M, Smith AT, Barbé J, Erill I. Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes. Nucleic Acids Res 2021; 49:11050-11066. [PMID: 34614190 PMCID: PMC8565304 DOI: 10.1093/nar/gkab773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/18/2021] [Accepted: 10/04/2021] [Indexed: 02/07/2023] Open
Abstract
Lesions to DNA compromise chromosome integrity, posing a direct threat to cell survival. The bacterial SOS response is a widespread transcriptional regulatory mechanism to address DNA damage. This response is coordinated by the LexA transcriptional repressor, which controls genes involved in DNA repair, mutagenesis and cell-cycle control. To date, the SOS response has been characterized in most major bacterial groups, with the notable exception of the Bacteroidetes. No LexA homologs had been identified in this large, diverse and ecologically important phylum, suggesting that it lacked an inducible mechanism to address DNA damage. Here, we report the identification of a novel family of transcriptional repressors in the Bacteroidetes that orchestrate a canonical response to DNA damage in this phylum. These proteins belong to the S24 peptidase family, but are structurally different from LexA. Their N-terminal domain is most closely related to CI-type bacteriophage repressors, suggesting that they may have originated from phage lytic phase repressors. Given their role as SOS regulators, however, we propose to designate them as non-canonical LexA proteins. The identification of a new class of repressors orchestrating the SOS response illuminates long-standing questions regarding the origin and plasticity of this transcriptional network.
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Affiliation(s)
- Miquel Sánchez-Osuna
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Mark Lee
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Jordi Barbé
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Ivan Erill
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain.,Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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Biswas A, Ghosh S, Sinha D, Dutta A, Seal S, Bagchi A, Sau S. Dimerization ability, denaturation mechanism, and the stability of a staphylococcal phage repressor and its two domains. Int J Biol Macromol 2019; 124:903-914. [DOI: 10.1016/j.ijbiomac.2018.11.263] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 11/29/2022]
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Murchland I, Ahlgren-Berg A, Priest DG, Dodd IB, Shearwin KE. Promoter activation by CII, a potent transcriptional activator from bacteriophage 186. J Biol Chem 2014; 289:32094-32108. [PMID: 25294872 DOI: 10.1074/jbc.m114.608026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The lysogeny promoting protein CII from bacteriophage 186 is a potent transcriptional activator, capable of mediating at least a 400-fold increase in transcription over basal activity. Despite being functionally similar to its counterpart in phage λ, it shows no homology at the level of protein sequence and does not belong to any known family of transcriptional activators. It also has the unusual property of binding DNA half-sites that are separated by 20 base pairs, center to center. Here we investigate the structural and functional properties of CII using a combination of genetics, in vitro assays, and mutational analysis. We find that 186 CII possesses two functional domains, with an independent activation epitope in each. 186 CII owes its potent activity to activation mechanisms that are dependent on both the σ(70) and α C-terminal domain (αCTD) components of RNA polymerase, contacting different functional domains. We also present evidence that like λ CII, 186 CII is proteolytically degraded in vivo, but unlike λ CII, 186 CII proteolysis results in a specific, transcriptionally inactive, degradation product with altered self-association properties.
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Affiliation(s)
- Iain Murchland
- Department of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Alexandra Ahlgren-Berg
- Department of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - David G Priest
- Department of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Ian B Dodd
- Department of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Keith E Shearwin
- Department of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia.
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7
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Biswas A, Mandal S, Sau S. The N-terminal domain of the repressor of Staphylococcus aureus phage Φ11 possesses an unusual dimerization ability and DNA binding affinity. PLoS One 2014; 9:e95012. [PMID: 24747758 PMCID: PMC3991615 DOI: 10.1371/journal.pone.0095012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 03/22/2014] [Indexed: 11/19/2022] Open
Abstract
Bacteriophage Φ11 uses Staphylococcus aureus as its host and, like lambdoid phages, harbors three homologous operators in between its two divergently oriented repressor genes. None of the repressors of Φ11, however, showed binding to all three operators, even at high concentrations. To understand why the DNA binding mechanism of Φ11 repressors does not match that of lambdoid phage repressors, we studied the N-terminal domain of the Φ11 lysogenic repressor, as it harbors a putative helix-turn-helix motif. Our data revealed that the secondary and tertiary structures of the N-terminal domain were different from those of the full-length repressor. Nonetheless, the N-terminal domain was able to dimerize and bind to the operators similar to the intact repressor. In addition, the operator base specificity, binding stoichiometry, and binding mechanism of this domain were nearly identical to those of the whole repressor. The binding affinities of the repressor and its N-terminal domain were reduced to a similar extent when the temperature was increased to 42°C. Both proteins also adequately dislodged a RNA polymerase from a Φ11 DNA fragment carrying two operators and a promoter. Unlike the intact repressor, the binding of the N-terminal domain to two adjacent operator sites was not cooperative in nature. Taken together, we suggest that the dimerization and DNA binding abilities of the N-terminal domain of the Φ11 repressor are distinct from those of the DNA binding domains of other phage repressors.
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Affiliation(s)
- Anindya Biswas
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Sukhendu Mandal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
- * E-mail:
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Wang H, Dodd IB, Dunlap DD, Shearwin KE, Finzi L. Single molecule analysis of DNA wrapping and looping by a circular 14mer wheel of the bacteriophage 186 CI repressor. Nucleic Acids Res 2013; 41:5746-56. [PMID: 23620280 PMCID: PMC3675496 DOI: 10.1093/nar/gkt298] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 02/26/2013] [Accepted: 03/28/2013] [Indexed: 11/29/2022] Open
Abstract
The lytic-lysogenic decision in bacteriophage 186 is governed by the 186 CI repressor protein in a unique way. The 186 CI is proposed to form a wheel-like oligomer that can mediate either wrapped or looped nucleoprotein complexes to provide the cooperative and competitive interactions needed for regulation. Although consistent with structural, biochemical and gene expression data, many aspects of this model are based on inference. Here, we use atomic force microscopy (AFM) to reveal the various predicted wrapped and looped species, and new ones, for CI regulation of lytic and lysogenic transcription. Automated AFM analysis showed CI particles of the predicted dimensions on the DNA, with CI multimerization favoured by DNA binding. Measurement of the length of the wrapped DNA segments indicated that CI may move on the DNA, wrapping or releasing DNA on either side of the wheel. Tethered particle motion experiments were consistent with wrapping and looping of DNA by CI in solution, where in contrast to λ repressor, the looped species were exceptionally stable. The CI regulatory system provides an intriguing comparison with that of nucleosomes, which share the ability to wrap and release similar sized segments of DNA.
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Affiliation(s)
- Haowei Wang
- Department of Physics, Emory University, 400 Dowman Drive, Atlanta, GA 30322, USA, School of Molecular and Biomedical Science, Discipline of Biochemistry, University of Adelaide, Adelaide 5005, Australia and Department of Cell Biology, Emory University, 615 Michael Street, Atlanta, GA 30322, USA
| | - Ian B. Dodd
- Department of Physics, Emory University, 400 Dowman Drive, Atlanta, GA 30322, USA, School of Molecular and Biomedical Science, Discipline of Biochemistry, University of Adelaide, Adelaide 5005, Australia and Department of Cell Biology, Emory University, 615 Michael Street, Atlanta, GA 30322, USA
| | - David D. Dunlap
- Department of Physics, Emory University, 400 Dowman Drive, Atlanta, GA 30322, USA, School of Molecular and Biomedical Science, Discipline of Biochemistry, University of Adelaide, Adelaide 5005, Australia and Department of Cell Biology, Emory University, 615 Michael Street, Atlanta, GA 30322, USA
| | - Keith E. Shearwin
- Department of Physics, Emory University, 400 Dowman Drive, Atlanta, GA 30322, USA, School of Molecular and Biomedical Science, Discipline of Biochemistry, University of Adelaide, Adelaide 5005, Australia and Department of Cell Biology, Emory University, 615 Michael Street, Atlanta, GA 30322, USA
| | - Laura Finzi
- Department of Physics, Emory University, 400 Dowman Drive, Atlanta, GA 30322, USA, School of Molecular and Biomedical Science, Discipline of Biochemistry, University of Adelaide, Adelaide 5005, Australia and Department of Cell Biology, Emory University, 615 Michael Street, Atlanta, GA 30322, USA
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Evolutionary link between the mycobacterial plasmid pAL5000 replication protein RepB and the extracytoplasmic function family of σ factors. J Bacteriol 2012; 194:1331-41. [PMID: 22247504 DOI: 10.1128/jb.06218-11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mycobacterial plasmid pAL5000 represents a family of plasmids found mostly in the Actinobacteria. It replicates using two plasmid-encoded proteins, RepA and RepB. While BLAST searches indicate that RepA is a replicase family protein, the evolutionary connection of RepB cannot be established, as no significant homologous partner (E < 10(-3)) outside the RepB family can be identified. To obtain insight into the structure-function and evolutionary connections of RepB, an investigation was undertaken using homology modeling, phylogenetic, and mutational analysis methods. The results indicate that although they are synthesized from the same operon, the phylogenetic affinities of RepA and RepB differ. Thus, the operon may have evolved through random breaking and joining events. Homology modeling predicted the presence of a three-helical helix-turn-helix domain characteristic of region 4 of extracytoplasmic function (ECF) σ factors in the C-terminal region of RepB. At the N-terminal region, there is a helical stretch, which may be distantly related to region 3 of σ factors. Mutational analysis identified two arginines indispensable for RepB activity, one each located within the C- and N-terminal conserved regions. Apart from analyzing the domain organization of the protein, the significance of the presence of a highly conserved A/T-rich element within the RepB binding site was investigated. Mutational analysis revealed that although this motif does not bind RepB, its integrity is important for efficient DNA-protein interactions and replication to occur. The present investigation unravels the possibility that RepB-like proteins and their binding sites represent ancient DNA-protein interaction modules.
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10
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Modeling of the genetic switch of bacteriophage TP901-1: A heteromer of CI and MOR ensures robust bistability. J Mol Biol 2009; 394:15-28. [PMID: 19747486 DOI: 10.1016/j.jmb.2009.08.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 08/23/2009] [Accepted: 08/27/2009] [Indexed: 11/22/2022]
Abstract
The lytic-lysogenic switch of the temperate lactococcal phage TP901-1 is fundamentally different from that of phage lambda. In phage TP901-1, the lytic promoter P(L) is repressed by CI, whereas repression of the lysogenic promoter P(R) requires the presence of both of the antagonistic regulator proteins, MOR and CI. We model the central part of the switch and compare the two cases for P(R) repression: the one where the two regulators interact only on the DNA and the other where the two regulators form a heteromer complex in the cytoplasm prior to DNA binding. The models are analyzed for bistability, and the predicted promoter repression folds are compared to experimental data. We conclude that the experimental data are best reproduced the latter case, where a heteromer complex forms in solution. We further find that CI sequestration by the formation of MOR:CI complexes in cytoplasm makes the genetic switch robust.
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Pedersen M, Hammer K. The role of MOR and the CI operator sites on the genetic switch of the temperate bacteriophage TP901-1. J Mol Biol 2008; 384:577-89. [PMID: 18930065 DOI: 10.1016/j.jmb.2008.09.071] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Revised: 09/22/2008] [Accepted: 09/23/2008] [Indexed: 10/21/2022]
Abstract
A genetic switch controls whether the temperate bacteriophage TP901-1 will enter a lytic or a lysogenic life cycle after infection of its host, Lactococcus lactis. We studied this bistable switch encoded in a small DNA fragment of 979 bp by fusing it to a reporter gene on a low-copy-number plasmid. The cloned DNA fragment contained the two divergently oriented promoters, P(R) and P(L), transcribing the lysogenic and lytic gene clusters; the two promoter-proximal genes, cI and mor; and the three CI operator sites, O(R), O(L) and O(D). We show that mor encodes a protein and that this protein in concert with CI is required for the bistability. Furthermore, interaction of CI at O(R) represses transcription from the lysogenic promoter, P(R). Thus, CI regulates its own transcription. Interaction of CI at O(L) represses transcription from the lytic promoter, P(L). The presence of only O(L) (absence of O(R) and O(D)) is enough to maintain a bistable system. The distantly located operator site, O(D), functions as a helper site by increasing binding of CI at O(R) and O(L). In the immune state, O(D) increases repression of the lytic promoter, P(L). Our results strongly support the model that a hexameric form of CI binds cooperatively to the three operator sites in the immune state forming a CI-DNA loop structure. Finally, we show that in the anti-immune state, repression of the lysogenic promoter is independent of the known CI operator sites but requires the presence of both CI and MOR.
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Affiliation(s)
- Margit Pedersen
- Center for Systems Microbiology, DTU BIOSYS, Technical University of Denmark, DK-2800 Lyngby,
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12
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Identification of Quaternary Structure and Functional Domains of the CI Repressor from Bacteriophage TP901-1. J Mol Biol 2008; 376:983-96. [DOI: 10.1016/j.jmb.2007.12.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Revised: 12/10/2007] [Accepted: 12/11/2007] [Indexed: 11/21/2022]
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13
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Ahlgren-Berg A, Henriksson-Peltola P, Sehlén W, Haggård-Ljungquist E. A comparison of the DNA binding and bending capacities and the oligomeric states of the immunity repressors of heteroimmune coliphages P2 and WPhi. Nucleic Acids Res 2007; 35:3167-80. [PMID: 17485481 PMCID: PMC1904263 DOI: 10.1093/nar/gkm171] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacteriophages P2 and WPhi are heteroimmune members of the P2-like family of temperate Escherichia coli phages. Temperate phages can grow lytically or form lysogeny after infection. A transcriptional switch that contains two con-vergent promoters, Pe and Pc, and two repressors regulate what life mode to enter. The immunity repressor C is the first gene of the lysogenic operon, and it blocks the early Pe promoter. In this work, some characteristics of the C proteins of P2 and WPhi are compared. An in vivo genetic analysis shows that WPhi C, like P2 C, has a strong dimerization activity in the absence of its DNA target. Both C proteins recognize two directly repeated sequences, termed half-sites and a strong bending is induced in the respective DNA target upon binding. P2 C is unable to bind to one half-site as opposed to WPhi, but both half-sites are required for repression of WPhi Pe. A reduction from three to two helical turns between the centers of the half-sites in WPhi has no significant effect on the capacity to repress Pe. However, the protein-DNA complexes formed differ, as determined by electrophoretic mobility shift experiments. A difference in spontaneous phage production is observed in isogenic lysogens.
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14
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Dodd IB, Shearwin KE, Sneppen K. Modelling transcriptional interference and DNA looping in gene regulation. J Mol Biol 2007; 369:1200-13. [PMID: 17498740 DOI: 10.1016/j.jmb.2007.04.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 04/10/2007] [Accepted: 04/11/2007] [Indexed: 11/25/2022]
Abstract
We describe a hybrid statistical mechanical and dynamical approach for modelling the formation of closed, open and elongating complexes of RNA polymerase, the interactions of these polymerases to produce transcriptional interference, and the regulation of these processes by a DNA-binding and DNA-looping regulatory protein. As a model system, we have used bacteriophage 186, for which genetic, biochemical and structural studies have suggested that the CI repressor binds as a 14-mer to form alternative DNA-looped complexes, and activates lysogenic transcription indirectly by relieving transcriptional interference caused by the convergent lytic promoter. The modelling showed that the original mechanisms proposed to explain this relief of transcriptional interference are not consistent with the available in vivo reporter data. However, a good fit to the reporter data was given by a revised model that incorporates a novel predicted regulatory mechanism: that RNA polymerase bound at the lysogenic promoter protects itself from transcriptional interference by recruiting CI to the lytic promoter. This mechanism and various estimates of in vivo biochemical parameters for the 186 CI system should be testable. Our results demonstrate the power of mathematical modelling for the extraction of detailed biochemical information from in vivo data.
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Affiliation(s)
- Ian B Dodd
- Centre for Models of Life, Niels Bohr Institute, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark.
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15
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Henriksson-Peltola P, Sehlén W, Haggård-Ljungquist E. Determination of the DNA-binding kinetics of three related but heteroimmune bacteriophage repressors using EMSA and SPR analysis. Nucleic Acids Res 2007; 35:3181-91. [PMID: 17412705 PMCID: PMC1904268 DOI: 10.1093/nar/gkm172] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Revised: 03/05/2007] [Accepted: 03/06/2007] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages P2, P2 Hy dis and WPhi are very similar but heteroimmune Escherichia coli phages. The structural genes show over 96% identity, but the repressors show between 43 and 63% identities. Furthermore, the operators, which contain two directly repeated sequences, vary in sequence, length, location relative to the promoter and spacing between the direct repeats. We have compared the in vivo effects of the wild type and mutated operators on gene expression with the complexes formed between the repressors and their wild type or mutated operators using electrophoretic mobility shift assay (EMSA), and real-time kinetics of the protein-DNA interactions using surface plasmon resonance (SPR) analysis. Using EMSA, the repressors formed different protein-DNA complexes, and only WPhi was significantly affected by point mutations. However, SPR analysis showed a reduced association rate constant and an increased dissociation rate constant for P2 and WPhi operator mutants. The association rate constants of P2 Hy dis was too fast to be determined. The P2 Hy dis dissociation response curves were shown to be triphasic, while both P2 and WPhi C were biphasic. Thus, the kinetics of complex formation and the nature of the complexes formed differ extensively between these very closely related phages.
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16
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Pinkett HW, Shearwin KE, Stayrook S, Dodd IB, Burr T, Hochschild A, Egan JB, Lewis M. The structural basis of cooperative regulation at an alternate genetic switch. Mol Cell 2006; 21:605-15. [PMID: 16507359 DOI: 10.1016/j.molcel.2006.01.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Revised: 12/12/2005] [Accepted: 01/12/2006] [Indexed: 01/04/2023]
Abstract
Bacteriophage lambda is a paradigm for understanding the role of cooperativity in gene regulation. Comparison of the regulatory regions of lambda and the unrelated temperate bacteriophage 186 provides insight into alternate ways to assemble functional genetic switches. The structure of the C-terminal domain of the 186 repressor, determined at 2.7 A resolution, reveals an unusual heptamer of dimers, consistent with presented genetic studies. In addition, the structure of a cooperativity mutant of the full-length 186 repressor, identified by genetic screens, was solved to 1.95 A resolution. These structures provide a molecular basis for understanding lysogenic regulation in 186. Whereas the overall fold of the 186 and lambda repressor monomers is remarkably similar, the way the two repressors cooperatively assemble is quite different and explains in part the differences in their regulatory activity.
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Affiliation(s)
- Heather W Pinkett
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 37th and Hamilton Walk, Philadelphia, 19102, USA
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17
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Ferenczi S, Orosz L, Papp PP. Repressor of Phage
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3
with Altered Binding Specificity Indicates Spatial Differences in Repressor-Operator Complexes. J Bacteriol 2006; 188:1663-6. [PMID: 16452452 PMCID: PMC1367245 DOI: 10.1128/jb.188.4.1663-1666.2006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
The C repressor protein of phage
16-3
, which is required for establishing and maintaining lysogeny, recognizes structurally different operators which differ by 2 bp in the length of the spacer between the conserved palindromic sequences. A “rotationally flexible protein homodimers” model has been proposed in order to explain the conformational adaptivity of the
16-3
repressor. In this paper, we report on the isolation of a repressor mutant with altered binding specificity which was used to identify a residue-base pair contact and to monitor the spatial relationship of the recognition helix of C repressor to the contacting major groove of DNA within the two kinds of repressor-operator complexes. Our results indicate spatial differences at the interface which may reflect different docking arrangements in recognition of the structurally different operators by the
16-3
repressor.
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Affiliation(s)
- Szilamér Ferenczi
- Institute of Genetics, Agricultural Biotechnology Center, Gödöllõ, Szent-Györgyi A. 4., H-2100, Hungary
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18
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Bourhy P, Frangeul L, Couvé E, Glaser P, Saint Girons I, Picardeau M. Complete nucleotide sequence of the LE1 prophage from the spirochete Leptospira biflexa and characterization of its replication and partition functions. J Bacteriol 2005; 187:3931-40. [PMID: 15937155 PMCID: PMC1151745 DOI: 10.1128/jb.187.12.3931-3940.2005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first and, to date, only extrachromosomal circular replicon identified in the spirochete Leptospira is the LE1 prophage from Leptospira biflexa. The 74-kb LE1 genome has a GC content of 36%, which is similar to the GC content of Leptospira spp. Most of the 79 predicted open reading frames (ORFs) showed no similarities to known ORFs. However 21 ORFs appeared to be organized in clusters that could code for head and tail structural proteins and immunity repressor proteins. In addition, the pattern of gene expression showed that several LE1 genes are expressed specifically either in LE1 prophage or in L. biflexa late after infection. Since the LE1 prophage replicates autonomously as a circular replicon in L. biflexa, we were able to engineer an L. biflexa-Escherichia coli shuttle vector from a 5.3-kb DNA fragment of LE1 (Saint Girons et al., J. Bacteriol. 182:5700-5705, 2000), opening this genus to genetic manipulation. In this study, base compositional asymmetry confirms the location of the LE1 replication region and suggests that LE1 replicates via a bidirectional Theta-like replication mechanism from this unique origin. By subcloning experiments, the replication region can be narrowed down to a 1-kb region. This minimal replication region consists of a rep encoding a protein of 180 amino acids. Upstream from rep, putative partitioning genes, called parA and parB, were found to be similar to the par loci in Borrelia plasmids. A significant increase of plasmid stability in L. biflexa can be seen only when both parA and parB are present. These results enable the construction of new shuttle vectors for studying the genetics of Leptospira spp. This study will also contribute to a better knowledge of phages unrelated to lambdoid phages.
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Affiliation(s)
- Pascale Bourhy
- Laboratoire des Spirochètes, Institut Pasteur, 25 rue du docteur Roux, 75724 Paris Cedex 15, France
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19
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Rich RL, Myszka DG. A survey of the year 2002 commercial optical biosensor literature. J Mol Recognit 2004; 16:351-82. [PMID: 14732928 DOI: 10.1002/jmr.649] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have compiled 819 articles published in the year 2002 that involved commercial optical biosensor technology. The literature demonstrates that the technology's application continues to increase as biosensors are contributing to diverse scientific fields and are used to examine interactions ranging in size from small molecules to whole cells. Also, the variety of available commercial biosensor platforms is increasing and the expertise of users is improving. In this review, we use the literature to focus on the basic types of biosensor experiments, including kinetics, equilibrium analysis, solution competition, active concentration determination and screening. In addition, using examples of particularly well-performed analyses, we illustrate the high information content available in the primary response data and emphasize the impact of including figures in publications to support the results of biosensor analyses.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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20
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Abstract
The non-lambdoid coliphage 186 provides an alternative model to the lytic-lysogenic switch of phage lambda. Like lambda, the key switch regulator, the CI repressor, associates to octamers. Unlike lambda, the lytic promoter (pR) and the lysogenic promoter (pL) are face-to-face, 62 bp apart and are flanked by distal CI binding sites (FL and FR) located approximately 300 bp away. Using reporter and footprinting studies, we show that the outcome, but not the mechanism, of regulation by 186 CI is very similar to lambda. 186 CI stimulates pL transcription indirectly by repressing convergent interfering transcription from pR. However, in the absence of the flanking FL and FR sites, CI bound at pR interacts co-operatively with a weak CI binding site at pL and represses both promoters. FL and FR play a critical role; they assist repression of pR and simultaneously alleviate repression of pL, thus allowing high pL activity. We propose that the 186 switch is regulated by a novel mechanism in which a CI octamer bound at pR forms alternative DNA loops to pL or to a flanking site, depending on CI concentration.
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Affiliation(s)
- Ian B Dodd
- Department of Molecular Biosciences (Biochemistry), University of Adelaide, South Australia, Australia.
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