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  1. Article ; Online: Call for Special Issue Papers:

    Hinton, Deborah M / Turner, Paul E

    PHAGE (New Rochelle, N.Y.)

    2022  Volume 3, Issue 1, Page(s) 1–2

    Language English
    Publishing date 2022-03-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2986345-4
    ISSN 2641-6549 ; 2641-6530
    ISSN (online) 2641-6549
    ISSN 2641-6530
    DOI 10.1089/phage.2022.29026.cfp
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A 3D puzzle approach to building protein-DNA structures.

    Hinton, Deborah M

    Transcription

    2017  Volume 8, Issue 2, Page(s) 113–119

    Abstract: Despite recent advances in structural analysis, it is still challenging to obtain a high-resolution structure for a complex of RNA polymerase, transcriptional factors, and DNA. However, using biochemical constraints, 3D printed models of available ... ...

    Abstract Despite recent advances in structural analysis, it is still challenging to obtain a high-resolution structure for a complex of RNA polymerase, transcriptional factors, and DNA. However, using biochemical constraints, 3D printed models of available structures, and computer modeling, one can build biologically relevant models of such supramolecular complexes.
    Language English
    Publishing date 2017-03-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2646974-1
    ISSN 2154-1272 ; 2154-1264
    ISSN (online) 2154-1272
    ISSN 2154-1264
    DOI 10.1080/21541264.2017.1283387
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Special Issue on Phage/Host Combat: Phage Strategies for Taking Over the Host and Host Strategies for Defenses.

    Clokie, Martha R J / Hinton, Deborah M

    PHAGE (New Rochelle, N.Y.)

    2022  Volume 3, Issue 3, Page(s) 125–126

    Language English
    Publishing date 2022-09-19
    Publishing country United States
    Document type Editorial
    ZDB-ID 2986345-4
    ISSN 2641-6549 ; 2641-6530
    ISSN (online) 2641-6549
    ISSN 2641-6530
    DOI 10.1089/phage.2022.29034.editorial
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: VpsR Directly Activates Transcription of Multiple Biofilm Genes in Vibrio cholerae.

    Hsieh, Meng-Lun / Waters, Christopher M / Hinton, Deborah M

    Journal of bacteriology

    2020  Volume 202, Issue 18

    Abstract: ... Vibrio ... ...

    Abstract Vibrio cholerae
    MeSH term(s) Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biofilms ; Cyclic GMP/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Gene Expression Regulation, Bacterial ; Operon ; Promoter Regions, Genetic ; Sigma Factor/metabolism ; Vibrio cholerae/genetics
    Chemical Substances Bacterial Proteins ; Sigma Factor ; VpsR protein, Vibrio cholerae ; RNA polymerase sigma 70 (EC 2.7.7.-) ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; Cyclic GMP (H2D2X058MU)
    Language English
    Publishing date 2020-08-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/JB.00234-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Ud II Zs.50: Show issues Location:
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  5. Article ; Online: Setting Up a Better Infection: Overexpression of the Early Bacteriophage T4 Gene

    Son, Bokyung / Patterson-West, Jennifer / Thompson, Christine O / Iben, James R / Hinton, Deborah M

    PHAGE (New Rochelle, N.Y.)

    2022  Volume 3, Issue 3, Page(s) 141–152

    Abstract: Background: :: Methods: :: Results: :: Conclusion: : ...

    Abstract Background: :
    Methods: :
    Results: :
    Conclusion: :
    Language English
    Publishing date 2022-09-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2986345-4
    ISSN 2641-6549 ; 2641-6530
    ISSN (online) 2641-6549
    ISSN 2641-6530
    DOI 10.1089/phage.2022.0023
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: The

    Arroyo-Mendoza, Melissa / Proctor, Alexandra / Correa-Medina, Abraham / Brand, Meghan Wymore / Rosas, Virginia / Wannemuehler, Michael J / Phillips, Gregory J / Hinton, Deborah M

    bioRxiv : the preprint server for biology

    2023  

    Abstract: LF82, an adherent ... ...

    Abstract LF82, an adherent invasive
    Language English
    Publishing date 2023-02-08
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.08.523653
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Combining Gel Retardation and Footprinting to Determine Protein-DNA Interactions of Specific and/or Less Stable Complexes.

    Hsieh, Meng-Lun / Boulanger, Alice / Knipling, Leslie G / Hinton, Deborah M

    Bio-protocol

    2020  Volume 10, Issue 23, Page(s) e3843

    Abstract: DNA footprinting is a classic technique to investigate protein-DNA interactions. However, traditional footprinting protocols can be unsuccessful or difficult to interpret if the binding of the protein to the DNA is weak, the protein has a fast off-rate, ... ...

    Abstract DNA footprinting is a classic technique to investigate protein-DNA interactions. However, traditional footprinting protocols can be unsuccessful or difficult to interpret if the binding of the protein to the DNA is weak, the protein has a fast off-rate, or if several different protein-DNA complexes are formed. Our protocol differs from traditional footprinting protocols, because it provides a method to isolate the protein-DNA complex from a native gel after treatment with the footprinting agent, thus removing the bound DNA from the free DNA or other protein-DNA complexes. The DNA is then extracted from the isolated complex before electrophoresis on a sequencing gel to determine the footprinting pattern. This analysis provides a possible solution for those who have been unable to use traditional footprinting methods to determine protein-DNA contacts.
    Language English
    Publishing date 2020-12-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325 ; 2331-8325
    ISSN (online) 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.3843
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Transcriptional control in the prereplicative phase of T4 development.

    Hinton, Deborah M

    Virology journal

    2010  Volume 7, Page(s) 289

    Abstract: Control of transcription is crucial for correct gene expression and orderly development. For many years, bacteriophage T4 has provided a simple model system to investigate mechanisms that regulate this process. Development of T4 requires the ... ...

    Abstract Control of transcription is crucial for correct gene expression and orderly development. For many years, bacteriophage T4 has provided a simple model system to investigate mechanisms that regulate this process. Development of T4 requires the transcription of early, middle and late RNAs. Because T4 does not encode its own RNA polymerase, it must redirect the polymerase of its host, E. coli, to the correct class of genes at the correct time. T4 accomplishes this through the action of phage-encoded factors. Here I review recent studies investigating the transcription of T4 prereplicative genes, which are expressed as early and middle transcripts. Early RNAs are generated immediately after infection from T4 promoters that contain excellent recognition sequences for host polymerase. Consequently, the early promoters compete extremely well with host promoters for the available polymerase. T4 early promoter activity is further enhanced by the action of the T4 Alt protein, a component of the phage head that is injected into E. coli along with the phage DNA. Alt modifies Arg265 on one of the two α subunits of RNA polymerase. Although work with host promoters predicts that this modification should decrease promoter activity, transcription from some T4 early promoters increases when RNA polymerase is modified by Alt. Transcription of T4 middle genes begins about 1 minute after infection and proceeds by two pathways: 1) extension of early transcripts into downstream middle genes and 2) activation of T4 middle promoters through a process called sigma appropriation. In this activation, the T4 co-activator AsiA binds to Region 4 of σ⁷⁰, the specificity subunit of RNA polymerase. This binding dramatically remodels this portion of σ⁷⁰, which then allows the T4 activator MotA to also interact with σ⁷⁰. In addition, AsiA restructuring of σ⁷⁰ prevents Region 4 from forming its normal contacts with the -35 region of promoter DNA, which in turn allows MotA to interact with its DNA binding site, a MotA box, centered at the -30 region of middle promoter DNA. T4 sigma appropriation reveals how a specific domain within RNA polymerase can be remolded and then exploited to alter promoter specificity.
    MeSH term(s) Bacteriophage T4/genetics ; Bacteriophage T4/physiology ; DNA Replication ; Escherichia coli/virology ; Gene Expression Regulation, Viral ; Host-Parasite Interactions ; Promoter Regions, Genetic ; RNA, Messenger/biosynthesis ; RNA, Viral/biosynthesis ; Transcription, Genetic ; Virus Replication
    Chemical Substances RNA, Messenger ; RNA, Viral
    Language English
    Publishing date 2010-10-28
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Intramural ; Review
    ISSN 1743-422X
    ISSN (online) 1743-422X
    DOI 10.1186/1743-422X-7-289
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Transcriptional control in the prereplicative phase of T4 development

    Hinton Deborah M

    Virology Journal, Vol 7, Iss 1, p

    2010  Volume 289

    Abstract: Abstract Control of transcription is crucial for correct gene expression and orderly development. For many years, bacteriophage T4 has provided a simple model system to investigate mechanisms that regulate this process. Development of T4 requires the ... ...

    Abstract Abstract Control of transcription is crucial for correct gene expression and orderly development. For many years, bacteriophage T4 has provided a simple model system to investigate mechanisms that regulate this process. Development of T4 requires the transcription of early, middle and late RNAs. Because T4 does not encode its own RNA polymerase, it must redirect the polymerase of its host, E. coli , to the correct class of genes at the correct time. T4 accomplishes this through the action of phage-encoded factors. Here I review recent studies investigating the transcription of T4 prereplicative genes, which are expressed as early and middle transcripts. Early RNAs are generated immediately after infection from T4 promoters that contain excellent recognition sequences for host polymerase. Consequently, the early promoters compete extremely well with host promoters for the available polymerase. T4 early promoter activity is further enhanced by the action of the T4 Alt protein, a component of the phage head that is injected into E. coli along with the phage DNA. Alt modifies Arg265 on one of the two α subunits of RNA polymerase. Although work with host promoters predicts that this modification should decrease promoter activity, transcription from some T4 early promoters increases when RNA polymerase is modified by Alt. Transcription of T4 middle genes begins about 1 minute after infection and proceeds by two pathways: 1) extension of early transcripts into downstream middle genes and 2) activation of T4 middle promoters through a process called sigma appropriation. In this activation, the T4 co-activator AsiA binds to Region 4 of σ 70 , the specificity subunit of RNA polymerase. This binding dramatically remodels this portion of σ 70 , which then allows the T4 activator MotA to also interact with σ 70 . In addition, AsiA restructuring of σ 70 prevents Region 4 from forming its normal contacts with the -35 region of promoter DNA, which in turn allows MotA to interact with its DNA binding site, a MotA box, centered at the -30 region of middle promoter DNA. T4 sigma appropriation reveals how a specific domain within RNA polymerase can be remolded and then exploited to alter promoter specificity.
    Keywords Microbiology ; QR1-502 ; Science ; Q ; DOAJ:Microbiology ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Medicine (General) ; R5-920 ; Medicine ; R ; DOAJ:Medicine (General) ; DOAJ:Health Sciences
    Subject code 572
    Language English
    Publishing date 2010-10-01T00:00:00Z
    Publisher BioMed Central
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: VpsR and cyclic di-GMP together drive transcription initiation to activate biofilm formation in Vibrio cholerae.

    Hsieh, Meng-Lun / Hinton, Deborah M / Waters, Christopher M

    Nucleic acids research

    2018  Volume 46, Issue 17, Page(s) 8876–8887

    Abstract: The small molecule cyclic di-GMP (c-di-GMP) is known to affect bacterial gene expression in myriad ways. In Vibrio cholerae in vivo, the presence of c-di-GMP together with the response regulator VpsR results in transcription from PvpsL, a promoter of ... ...

    Abstract The small molecule cyclic di-GMP (c-di-GMP) is known to affect bacterial gene expression in myriad ways. In Vibrio cholerae in vivo, the presence of c-di-GMP together with the response regulator VpsR results in transcription from PvpsL, a promoter of biofilm biosynthesis genes. VpsR shares homology with enhancer binding proteins that activate σ54-RNA polymerase (RNAP), but it lacks conserved residues needed to bind to σ54-RNAP and to hydrolyze adenosine triphosphate, and PvpsL transcription does not require σ54 in vivo. Consequently, the mechanism of this activation has not been clear. Using an in vitro transcription system, we demonstrate activation of PvspL in the presence of VpsR, c-di-GMP and σ70-RNAP. c-di-GMP does not significantly change the affinity of VpsR for PvpsL DNA or the DNase I footprint of VpsR on the DNA, and it is not required for VpsR to dimerize. However, DNase I and KMnO4 footprints reveal that the σ70-RNAP/VpsR/c-di-GMP complex on PvpsL adopts a different conformation from that formed by σ70-RNAP alone, with c-di-GMP or with VpsR. Our results suggest that c-di-GMP is required for VpsR to generate the specific protein-DNA architecture needed for activated transcription, a previously unrecognized role for c-di-GMP in gene expression.
    MeSH term(s) Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/physiology ; Biofilms/growth & development ; Cyclic GMP/analogs & derivatives ; Cyclic GMP/physiology ; DNA Footprinting ; DNA, Bacterial/genetics ; DNA, Bacterial/metabolism ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/physiology ; DNA-Directed RNA Polymerases/metabolism ; Enzyme Activation ; Gene Expression Regulation, Bacterial/genetics ; Promoter Regions, Genetic/genetics ; Protein Binding ; Sigma Factor/metabolism ; Structure-Activity Relationship ; Transcription Initiation, Genetic ; Vibrio cholerae/genetics ; Vibrio cholerae/metabolism
    Chemical Substances Bacterial Proteins ; DNA, Bacterial ; DNA-Binding Proteins ; Sigma Factor ; VpsR protein, Vibrio cholerae ; bis(3',5')-cyclic diguanylic acid (61093-23-0) ; RNA polymerase sigma 70 (EC 2.7.7.-) ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; Cyclic GMP (H2D2X058MU)
    Language English
    Publishing date 2018-07-13
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gky606
    Database MEDical Literature Analysis and Retrieval System OnLINE

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