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Shi J, Wen A, Zhao M, You L, Zhang Y, Feng Y. Structural basis of σ appropriation. Nucleic Acids Res 2019; 47:9423-9432. [PMID: 31392983 PMCID: PMC6755090 DOI: 10.1093/nar/gkz682] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 01/25/2023] Open
Abstract
Bacteriophage T4 middle promoters are activated through a process called σ appropriation, which requires the concerted effort of two T4-encoded transcription factors: AsiA and MotA. Despite extensive biochemical and genetic analyses, puzzle remains, in part, because of a lack of precise structural information for σ appropriation complex. Here, we report a single-particle cryo-electron microscopy (cryo-EM) structure of an intact σ appropriation complex, comprising AsiA, MotA, Escherichia coli RNA polymerase (RNAP), σ70 and a T4 middle promoter. As expected, AsiA binds to and remodels σ region 4 to prevent its contact with host promoters. Unexpectedly, AsiA undergoes a large conformational change, takes over the job of σ region 4 and provides an anchor point for the upstream double-stranded DNA. Because σ region 4 is conserved among bacteria, other transcription factors may use the same strategy to alter the landscape of transcription immediately. Together, the structure provides a foundation for understanding σ appropriation and transcription activation.
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Affiliation(s)
- Jing Shi
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Aijia Wen
- Department of Biophysics, and Department of Pathology 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
| | - Linlin You
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Feng
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
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2
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Cuypers MG, Robertson RM, Knipling L, Waddell MB, Moon K, Hinton DM, White SW. The phage T4 MotA transcription factor contains a novel DNA binding motif that specifically recognizes modified DNA. Nucleic Acids Res 2019; 46:5308-5318. [PMID: 29718457 PMCID: PMC6007404 DOI: 10.1093/nar/gky292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 04/12/2018] [Indexed: 11/12/2022] Open
Abstract
During infection, bacteriophage T4 produces the MotA transcription factor that redirects the host RNA polymerase to the expression of T4 middle genes. The C-terminal 'double-wing' domain of MotA binds specifically to the MotA box motif of middle T4 promoters. We report the crystal structure of this complex, which reveals a new mode of protein-DNA interaction. The domain binds DNA mostly via interactions with the DNA backbone, but the binding is enhanced in the specific cognate structure by additional interactions with the MotA box motif in both the major and minor grooves. The linker connecting the two MotA domains plays a key role in stabilizing the complex via minor groove interactions. The structure is consistent with our previous model derived from chemical cleavage experiments using the entire transcription complex. α- and β-d-glucosyl-5-hydroxymethyl-deoxycytosine replace cytosine in T4 DNA, and docking simulations indicate that a cavity in the cognate structure can accommodate the modified cytosine. Binding studies confirm that the modification significantly enhances the binding affinity of MotA for the DNA. Consequently, our work reveals how a DNA modification can extend the uniqueness of small DNA motifs to facilitate the specificity of protein-DNA interactions.
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Affiliation(s)
- Maxime G Cuypers
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Rosanna M Robertson
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Leslie Knipling
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - M Brett Waddell
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kyung Moon
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Deborah M Hinton
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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Hinton DM. Transcriptional control in the prereplicative phase of T4 development. Virol J 2010; 7:289. [PMID: 21029433 PMCID: PMC2988021 DOI: 10.1186/1743-422x-7-289] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 10/28/2010] [Indexed: 12/18/2022] Open
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.
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Affiliation(s)
- Deborah M Hinton
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 8, Room 2A-13, Bethesda, MD 20892-0830, USA.
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Stoskiene G, Truncaite L, Zajanckauskaite A, Nivinskas R. Middle promoters constitute the most abundant and diverse class of promoters in bacteriophage T4. Mol Microbiol 2007; 64:421-34. [PMID: 17371501 DOI: 10.1111/j.1365-2958.2007.05659.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The temporally regulated transcription program of bacteriophage T4 relies upon the sequential utilization of three classes of promoters: early, middle and late. Here we show that middle promoters constitute perhaps the largest and the most diverse class of T4 promoters. In addition to 45 T4 middle promoters known to date, we mapped 13 new promoters, 10 of which deviate from the consensus MotA box, with some of them having no obvious match to it. So, 30 promoters of 58 identified now deviate from the consensus sequence deduced previously. In spite of the differences in their sequences, the in vivo activities of these T4 middle promoters were demonstrated to be dependent on both activators, MotA and AsiA. Traditionally, the MotA box was restricted to a 9 bp sequence with the highly conserved motif TGCTT. New logo based on the sequences of currently known middle promoters supports the conclusion that the consensus MotA box is comprised of 10 bp with the highly conserved central motif GCT. However, some apparently good matches to the consensus of middle promoters do not produce transcripts either in vivo or in vitro, indicating that the consensus sequence alone does not fully define a middle promoter.
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Affiliation(s)
- Giedre Stoskiene
- Department of Gene Engineering, Institute of Biochemistry, Mokslininku 12, 08662 Vilnius, Lithuania
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Truncaite L, Zajanckauskaite A, Arlauskas A, Nivinskas R. Transcription and RNA processing during expression of genes preceding DNA ligase gene 30 in T4-related bacteriophages. Virology 2006; 344:378-90. [PMID: 16225899 DOI: 10.1016/j.virol.2005.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Revised: 07/01/2005] [Accepted: 09/02/2005] [Indexed: 10/25/2022]
Abstract
Early gene expression in bacteriophage T4 is controlled primarily by the unique early promoters, while T4-encoded RegB endoribonuclease promotes degradation of many early messages contributing to the rapid shift of gene expression from the early to middle stages. The regulatory region for the genes clustered upstream of DNA ligase gene 30 of T4 was known to carry two strong early promoters and two putative RegB sites. Here, we present the comparative analysis of the regulatory events in this region of 16 T4-type bacteriophages. The regulatory elements for control of this gene cluster, such as rho-independent terminator, at least one early promoter, the sequence for stem-loop structure, and the RegB cleavage sites have been found to be conserved in the phages studied. Also, we present experimental evidence that the initial cleavage by RegB of phages TuIa and RB69 enables degradation of early phage mRNAs by the major Escherichia coli endoribonuclease, RNase E.
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Affiliation(s)
- Lidija Truncaite
- Department of Gene Engineering, Institute of Biochemistry, Mokslininku 12, 08662 Vilnius, Lithuania
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Hinton DM, Pande S, Wais N, Johnson XB, Vuthoori M, Makela A, Hook-Barnard I. Transcriptional takeover by σ appropriation: remodelling of the σ 70 subunit of Escherichia coli RNA polymerase by the bacteriophage T4 activator MotA and co-activator AsiA. Microbiology (Reading) 2005; 151:1729-1740. [PMID: 15941982 DOI: 10.1099/mic.0.27972-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Activation of bacteriophage T4 middle promoters, which occurs about 1 min after infection, uses two phage-encoded factors that change the promoter specificity of the host RNA polymerase. These phage factors, the MotA activator and the AsiA co-activator, interact with theσ70specificity subunit ofEscherichia coliRNA polymerase, which normally contacts the −10 and −35 regions of host promoter DNA. Like host promoters, T4 middle promoters have a good match to the canonicalσ70DNA element located in the −10 region. However, instead of theσ70DNA recognition element in the promoter's −35 region, they have a 9 bp sequence (a MotA box) centred at −30, which is bound by MotA. Recent work has begun to provide information about the MotA/AsiA system at a detailed molecular level. Accumulated evidence suggests that the presence of MotA and AsiA reconfigures protein–DNA contacts in the upstream promoter sequences, without significantly affecting the contacts ofσ70with the −10 region. This type of activation, which is called ‘σappropriation’, is fundamentally different from other well-characterized models of prokaryotic activation in which an activator frequently serves to forceσ70to contact a less than ideal −35 DNA element. This review summarizes the interactions of AsiA and MotA withσ70, and discusses how these interactions accomplish the switch to T4 middle promoters by inhibiting the typical contacts of the C-terminal region ofσ70, region 4, with the host −35 DNA element and with other subunits of polymerase.
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Affiliation(s)
- Deborah M Hinton
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Suchira Pande
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Neelowfar Wais
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Xanthia B Johnson
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Madhavi Vuthoori
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anna Makela
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - India Hook-Barnard
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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Truncaite L, Piesiniene L, Kolesinskiene G, Zajanckauskaite A, Driukas A, Klausa V, Nivinskas R. Twelve new MotA-dependent middle promoters of bacteriophage T4: consensus sequence revised. J Mol Biol 2003; 327:335-46. [PMID: 12628241 DOI: 10.1016/s0022-2836(03)00125-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Bacteriophage T4 middle-mode transcription requires Escherichia coli RNA polymerase, phage-encoded transcriptional activator MotA and co-activator AsiA that form a complex at a middle promoter DNA. T4 middle promoters have been defined by a consensus sequence deduced from the list of 14 middle promoters identified in earlier studies. To date, 33 middle promoters have been mapped on the T4 genome. Of these, 12 contain differences even at the highly conserved positions of the consensus sequence. In the T4 prereplicative gene cluster between genes e and rpbA, we have identified 12 new middle promoters, most of which contain differences from the consensus sequence deduced previously. Analysis of base conservation in the different sequence positions of new middle promoters, as well as those identified previously, revealed some new features of middle T4 promoters. We propose to define these promoters by a MotA box (a/t)(a/t)(a/t)TGCTTtA centred at the position -30, the sequence TAtaAT centred at -10 relative to the transcriptional start site, and the spacer region of 12(+/-1) base-pairs between them.
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Affiliation(s)
- Lidija Truncaite
- Department of Gene Engineering, Institute of Biochemistry, Mokslininku 12, 2600 Vilnius, Lithuania
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Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Rüger W. Bacteriophage T4 genome. Microbiol Mol Biol Rev 2003; 67:86-156, table of contents. [PMID: 12626685 PMCID: PMC150520 DOI: 10.1128/mmbr.67.1.86-156.2003] [Citation(s) in RCA: 562] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages-the most abundant and among the most ancient biological entities on Earth.
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Affiliation(s)
- Eric S Miller
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695-7615, USA.
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