Structure of IRF-1 with bound DNA reveals determinants of interferon regulation

Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, New York 10029, USA.
Nature (Impact Factor: 41.46). 02/1998; 391(6662):103-6. DOI: 10.1038/34224
Source: PubMed


The family of interferon regulatory factor (IRF) transcription factors is important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. The IRF family is characterized by a unique 'tryptophan cluster' DNA-binding region. Here we report the crystal structure of the IRF-1 region bound to the natural positive regulatory domain I (PRD I) DNA element from the interferon-beta promoter. The structure provides the first three-dimensional view of a member of the growing IRF family, revealing a new helix-turn-helix motif that latches onto DNA through three of the five conserved tryptophans. The motif selects a short GAAA core sequence through an obliquely angled recognition helix, with an accompanying bending of the DNA axis in the direction of the protein. Together, these features suggest a basis for the occurrence of GAAA repeats within IRF response elements and provide clues to the assembly of the higher-order interferon-beta enhancesome.

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    • "This molecule too has a conserved structure which is comprised of a well-defined DNAB in addition to an IRF-association domain (IAD) [24]. The DNAB domain is highly conserved across different species and includes 5 conserved tryptophan residues, while the IAD is much more diverse and works as regulatory domain known to associate with distinct transcription factors [25] "
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    ABSTRACT: Mammalian IRF9 and STAT2, together with STAT1, form the ISGF3 transcription factor complex, which is critical for type I interferon (IFN)-induced signaling, while IFNγ stimulation is mediated by homodimeric STAT1 protein. Teleost fish are known to possess most JAK and STAT family members, however, description of their functional activity in lower vertebrates is still scarce. In the present study we have identified two different STAT2 homologs and one IRF9 homolog from Atlantic salmon (Salmo salar). Both proteins have domain-like structures with functional motifs that are similar to higher vertebrates, suggesting that they are orthologs to mammalian STAT2 and IRF9. The two identified salmon STAT2s, named STAT2a and STAT2b, showed high sequence identity but were divergent in their transactivation domain (TAD). Like STAT1, ectopically expressed STAT2a and b were shown to be tyrosine phosphorylated by type I IFNs and, interestingly, also by IFNγ. Microscopy analyses demonstrated that STAT2 co-localized with STAT1a in the cytoplasm of unstimulated cells, while IFNa1 and IFNγ stimulation seemed to favor their nuclear localization. Overexpression of STAT2a or STAT2b together with STAT1a activated a GAS-containing reporter gene construct in IFNγ-stimulated cells. The highest induction of GAS promoter activation was found in IFNγ-stimulated cells transfected with IRF9 alone. Taken together, these data suggest that salmon STAT2 and IRF9 may have a role in IFNγ-induced signaling and promote the expression of GAS-driven genes in bony fish. Since mammalian STAT2 is primarily an ISGF3 component and not involved in IFNγ signaling, our finding features a novel role for STAT2 in fish.
    FEBS Open Bio 10/2014; 4. DOI:10.1016/j.fob.2014.09.007 · 1.52 Impact Factor
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    • "IFN-γ induces the JAK/STAT pathway leading to the activation and binding of transcriptional activators that induce expression of IFN-stimulated genes, notably IRF-1. IRF-1 is expressed at low levels in unstimulated cells and recognizes the ISRE found in most IFN-inducible gene promoters containing repeating short GAAA core sequences [4,5]. We have previously shown that CEACAM1 transcription can be induced by IFN-γ via an ISRE in the CEACAM1 promoter [6-8]. "
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    ABSTRACT: Interferon regulatory factor-1 (IRF-1) is a master regulator of IFN-gamma induced gene transcription. Previously we have shown that IRF-1 transcriptionally induces CEACAM1 via an ISRE (Interferon-Stimulated Response Element) in its promoter. CEACAM1 pre-mRNA undergoes extensive alternative splicing (AS) generating isoforms to produce either a short (S) cytoplasmic domain expressed primarily in epithelial cells or as an ITIM-containing long (L) isoform in immune cells. The transcriptional and molecular mechanism of CEACAM1 minigenes AS containing promoter ISREs mutations in the breast epithelial, MDA-MB-468, cell line was detected using flow cytometry. In addition, transcriptome sequencing was utilized to determine whether IRF-1 could direct the AS of other genes as well. Tumor xenografts were used to evaluate CEACAM1 isoform expression on the leading edge of breast tumor cells. In the present study, we provide evidence that CEACAM1's promoter and variable exon 7 cross-talk allowing IRF-1 to direct AS events. Transcriptome sequencing shows that IRF-1 can also induce the global AS of genes involved in regulation of growth and differentiation as well as genes of the cytokine family. Furthermore, MDA-MB-468 cells grown as tumor xenografts exhibit an AS switch to the L-isoform of CEACAM1, demonstrating that an in vivo inflammatory milieu is also capable of generating the AS switch, similar to that found in human breast cancers [1]. The novel AS regulatory activities attributed to IRF-1 indicate that the IFN-gamma response involves a global change in both gene transcription and AS in breast epithelial cells.
    Molecular Cancer 03/2014; 13(1):64. DOI:10.1186/1476-4598-13-64 · 4.26 Impact Factor
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    • "Their respective IRF proteins share significant homologies at the N-terminal 115 amino acids where they share a conserved tryptophan pentad repeat DNA-binding domain [20]. These include a DNA-binding domain of five tryptophan repeats of which three recognize the GAAA and AANNNGAA sequence motifs, that is, the IFN-stimulated response elements [20]. However, the variable domains at the C-terminus determine the functional specificity of the nine IRFs, their potential to interact with each other via IRF-association domains, and their cell type-specific actions [21] (Figure 1). "
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    ABSTRACT: The mononuclear phagocyte system regulates tissue homeostasis as well as all phases of tissue injury and repair. To do so changing tissue environments alter the phenotype of tissue macrophages to assure their support for sustaining and amplifying their respective surrounding environment. Interferon-regulatory factors are intracellular signaling elements that determine the maturation and gene transcription of leukocytes. Here we discuss how several among the 9 interferon-regulatory factors contribute to macrophage polarization.
    Mediators of Inflammation 11/2013; 2013:731023. DOI:10.1155/2013/731023 · 3.24 Impact Factor
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