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The ameliorative effects of α7 nicotinic acetylcholine receptor (α7nAChR) agonists have been demonstrated in acute kidney injury (AKI) caused by multiple stimulations. However, the ameliorative effect of α7nAChR on sepsis-induced acute kidney injury (SAKI) in the cecal ligation and puncture (CLP) model is unclear. Previous studies have demonstrated that α7nAChR is highly expressed on the surface of CD4+CD25+ regulatory T cells (Tregs). However, the role of Tregs in SAKI is unclear. We hypothesized that Tregs might play a role in the ameliorative effect of α7nAChR on SAKI. Hence, in this study, we determined the effects of PNU-282987 (a selective α7nAchR agonist) on SAKI and evaluated whether PNU-282987 would attenuate SAKI via regulating Tregs. Our study showed that immediate administration of PNU-282987 after CLP surgery in rats improved renal function, reduced levels of systemic inflammatory factors (tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), etc.), inflammatory cell infiltration and tubular apoptosis in renal tissues, and increased forkhead/winged helix transcription factor p3 (Foxp3) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) expression indicating activated Tregs. Moreover, in in vitro experiments, isolated Tregs co-cultured with PNU-282987 also displayed enhanced expression of CTLA-4 and Foxp3. Furthermore, Tregs were co-cultured with PNU-282987 for 24 hours and then reinfused into rats through the tail vein immediately after CLP surgery, and a significant renal protective effect was observed 24 hours postoperatively. These results demonstrate that PNU-282987 exerts its renal protective effects on SAKI through activation of Tregs.

Rpc34 is a subunit of the Rpc82/34/31 subcomplex residing on the DNA-binding cleft of RNA polymerase (Pol) III. Rpc34 contains a structurally flexible N-terminal tandem winged-helix (tWH) domain related to the TFIIE transcription factor. While the second WH (WH2) fold of the tWH domain is known to function in DNA melting activity during transcription initiation, the functional role of the WH1 fold is unknown. In this study, we generated a series of new Rpc34 tWH mutants conferring a cold-sensitive growth phenotype. We found that the tWH mutations severely compromised in vitro transcription activity due to destabilization of the preinitiation complex (PIC). Site-specific protein photo-cross-linking analysis indicated that the tWH domain persistently interacts with protein subunits of the Pol III cleft in the PIC and the ternary elongation complex (TEC). Furthermore, purified Pol III proteins with tWH mutations also showed reduced efficiency in RNA elongation. Our study results suggest that the tWH domain is an important protein module above the Pol III cleft that integrates protein and nucleic acid interactions for initiation and elongation.

Seven families of double-stranded DNA viruses have been identified, among which the Fuselloviridae and Rudiviridae are the most well-studied specimens and therefore represent model systems for detailed studies of archaeal virus biology. Two distinct genetic elements, SSV2 and pSSVx, belong to Fuselloviridae and coexist in the same Sulfolobus islandicus REY15/4 host, thus representing one of the few known two-virus systems in Archaea (1). pSSVx is a satellite virus that generates virus particles with the help of SSV2-associated packaging mechanisms. The transcriptional pattern of pSSVx undergoes a temporal variation of gene expression during its own life cycle, thus providing a good model for studying regulation of gene expression in Archaea (2). This genetic element encodes four TFs possibly implicated in the regulation of gene expression, i.e. ORF-c68, ORF51, ORF91 and ORF76. Among these, ORF76, here named Stf76 (Sulfolobus transcription factor 76 aminoacid protein), has homologs in almost all conjugative and cryptic plasmids from Sulfolobus (3), thus suggesting a relevant role for this protein in replication and/or maintenance of the plasmid. In this study, we have performed a detailed structural and functional characterization of Stf76. The corresponding gene has been cloned, expressed in Escherichia coli and the recombinant protein purified to homogeneity. To elucidate its interaction with the identified DNA operator sequence, analyses regarding its DNA binding capabilities by means of EMSA, circular dichroism, spectrofluorimetric and isothermal titration calorimetry experiments have been performed. Moreover, a structural study has been undertaken by Nuclear Magnetic Resonance spectroscopy leading to:(i) the solution structure of Stf76 based on CS-Rosetta approach, (ii) the characterization of the Stf76-DNA interaction by chemical shift perturbation analysis, (iii) a structural model describing the interaction of a single Stf76 monomer with its DNA operator. Altogether these results contribute to elucidate the regulatory mechanism underpinning the role of this protein (4). REFERENCES: 1. ARNOLD, H.P., ET AL.(1999) THE GENETIC ELEMENT PSSVX OF THE EXTREMELY THERMOPHILIC CRENARCHAEON SULFOLOBUS IS A HYBRID BETWEEN A PLASMID AND A VIRUS. MOL MICROBIOL, 34, 217-226. 2. CONTURSI, P., ET.AL. (2010) TRANSCRIPTION TERMINATION IN THE PLASMID/VIRUS HYBRID PSSVX FROM SULFOLOBUS ISLANDICUS. EXTREMOPHILES, 14, 453-463. 3. LIPPS, G. (2006) PLASMIDS AND VIRUSES OF THE THERMOACIDOPHILIC CRENARCHAEOTE SULFOLOBUS. EXTREMOPHILES, 10, 17-28. 4. CONTURSI P., FARINA B., PIRONE L. ET AL. NUCLEIC ACIDS RES. ACCEPTED 28 FEB. 2014.

BldD regulates transcription of key developmental genes in Streptomyces coelicolor. While the N-terminal domain is responsible for both dimerization and DNA binding, the structural and functional roles of the C-terminal domain (CTD) remain largely unexplored. Here, the solution structure of the BldD-CTD shows a novel winged-helix domain fold not compatible with DNA binding, due to the negatively charged surface and presence of an additional helix. Meanwhile, a small elongated groove with conserved hydrophobic patches surrounded by charged residues suggests that the BldD-CTD could be involved in protein-protein interactions that provide transcriptional regulation.

The winged helix domain (WHD) is a widespread nucleic-acid-binding protein structural element found in all kingdoms of life. Although the overall structure of the WHD is conserved, its functional properties and interaction profiles are extremely versatile. WHD-containing proteins can exploit nearly the full spectrum of nucleic acid structural features for recognition and even covalent modification or noncovalent rearrangement of target molecules. WHD functions range from sequence-recognizing keys in transcription factors and bulldozer-like strand-separating wedges in helicases to mediators of protein-protein interactions (PPIs). Further investigations are needed to understand the contribution of WHD structural dynamics to nucleic-acid-modifying enzymatic functions.

Homeobox genes, such as the Hox, Parahox and Nkx genes, are examples of conserved developmental regulatory genes. They are arranged into clusters that have been conserved over hundreds of millions of years of animal evolution [1–3]. Ancient clustering has also been suggested for the Wnt genes [4] but not for other transcription factor genes. Here, we focus on the evolution of Fox genes, which encode winged helix transcription factors with roles in metabolism, development and disease [5,6]. We demonstrate that four genes encoding Fox transcription factors are linked in insects and chordates and were most likely arranged into a gene cluster in basal bilaterians.

The surfaces of many bacteria feature pili or fimbriae, proteinaceous filaments that play an integral role in the adhesion of bacteria to host cells and, hence, in their pathogenicity.1,2 These extracellular structures are key virulence factors and potential targets for antibacterial drug and vaccine development. In certain Salmonella enterobacteria strains, one such class of fimbriae, the virulence plasmid-encoded fimbriae encoded by the pef operon,3,4 has been shown to be important for adhesion to murine small intestine and fluid accumulation,5 as well as biofilm formation on eukaryotic cell surfaces.6 Transcription of the pef operon, induced under acidic conditions, is modulated by the PefI regulatory protein.7 PefI represses plasmid-encoded fimbrial protein production by activating the leucine-responsive regulatory protein (Lrp) mediated inhibition of DNA methylation within the pef promoter region.7 PefI expression also inhibits transcription of flagellar proteins and consequently cell motility.8 Here we present the solution NMR structure of the 70-residue PefI transcription regulator from Salmonella enterica serovar Typhimurium LT2 [UniProtKB/TrEMBL ID, Q04822_SALTY; NESG ID, StR82; hereafter referred to as stPefI], a member of the FaeA-like protein domain family (Pfam identifier, PF04703). The sequence alignment of stPefI with its functional homolog in Escherichia coli, PapI, is shown in Fig. 1(A). We demonstrate that the structure of stPefI adopts a winged helix-turn-helix motif,9,10 consistent with its role as a DNA-binding transcriptional regulator. Moreover, in spite of their relatively low sequence identity (29%), the structure of stPefI is highly similar to that of E. coli PapI,11 which activates the expression of pyelonephritis-associated pili.12,13 Fig. 1 (A) Structure-based sequence alignment of stPefI and E. coli PapI (ecPapI). The sequence numbering for stPefI and the secondary structural elements found in its solution NMR structure (PDB ID, 2JT1) are shown above the alignment; t, turn and l, loop. ... Materials and Methods Isotopically enriched samples of stPefI were cloned, expressed, and purified, and the sample buffer was optimized for NMR studies following standard protocols of the NESG consortium;14,15 see Supplementary Material for a complete description of the methods used in this work. Briefly, samples of [U-13C,15N]- and [U-5%-13C,100%-15N]-stPefI for NMR spectroscopy were concentrated by ultracentrifugation to 0.5 to 0.7 mM in 95% H2O / 5% 2H2O solution containing 20 mM ammonium acetate, 450 mM NaCl, 10 mM DTT, 5 mM CaCl2 at pH 5.5. Analytical gel filtration chromatography, static light scattering (Supplementary Fig. S1) and one-dimensional 15N T1 and T2 relaxation data (Supplementary Fig. S2) demonstrate that the protein is monomeric under the conditions used in the NMR studies. All NMR data for resonance assignment and structure determination were collected at 20 °C on Bruker AVANCE 600 and 800 MHz spectrometers equipped with conventional 5-mm TXI probes, and a Varian INOVA 600 MHz instrument with a 5-mm HCN cold probe, and referenced to internal DSS (2,2-dimethyl-2-silapentane-5-sulfonic acid). Complete 1H, 13C, and 15N resonance assignments for stPefI were determined using conventional triple resonance NMR methods, with automated backbone assignment made by AutoAssign 2.4.0,16 followed by manual side chain assignment. Resonance assignments were validated using the Assignment Validation Suite (AVS) software package17 and deposited in the BioMagResDB (BMRB accession number, 15386). The solution NMR structure of stPefI was calculated using CYANA 2.1,18,19 and the 20 structures with lowest target function out of 100 in the final cycle were further refined by restrained molecular dynamics in explicit water using CNS 1.2.20,21 Structural statistics and global structure quality factors were computed using the PSVS 1.4 suite of structure quality assessment programs.22 The global goodness-of-fit of the final structure ensemble with the NOESY peak list data was determined using the RPF analysis program.23 The final ensemble of 20 models (excluding the C-terminal His6) were deposited into the Protein Data Bank (PDB ID, 2JT1). All structure figures were rendered using PyMOL (www.pymol.org).

The genetic analysis of the Foxa genes in both total and conditional mutant mice has clearly established that organogenesis of multiple systems is controlled by this subfamily of winged helix transcription factors. These discoveries followed the establishment of the conceptional framework of the mechanism of action of the FoxA proteins as “pioneer factors” that can engage chromatin before other transcription factors. Recent molecular and genomic studies have also shown that FoxA proteins can facilitate binding of several nuclear receptors to their respective targets in a context-dependent manner, greatly increasing the range and importance of FoxA factors in biology.

The eubacterial SOS system is a paradigm of cellular DNA damage and repair, and its activation can contribute to antibiotic resistance. Under normal conditions, LexA represses the transcription of many DNA repair proteins by binding to SOS 'boxes' in their operators. Under genotoxic stress, accumulating complexes of RecA, ATP and single-stranded DNA (ssDNA) activate LexA for autocleavage. To address how LexA recognizes its binding sites, we determined three crystal structures of Escherichia coli LexA in complex with SOS boxes. Here we report the structure of these LexA-DNA complexes. The DNA-binding domains of the LexA dimer interact with the DNA in the classical fashion of a winged helix-turn-helix motif. However, the wings of these two DNA-binding domains bind to the same minor groove of the DNA. These wing-wing contacts may explain why the spacing between the two half-sites of E. coli SOS boxes is invariant.

A P element enhancer trap screen was conducted to identify genes involved in dorsal-ventral boundary formation in Drosophila. The son of Notch (son) gene was identified by the son(2205) enhancer trap insertion, which is a partial loss-of-function mutation. Based on son(2205) mutant phenotypes and genetic interactions with Notch and wingless mutations, we conclude that son participates in wing development, and functions in the Notch signaling pathway at the dorsal-ventral boundary in the wing. Notch signaling pathway components activate son enhancer trap expression in wing cells. son enhancer trap expression is regulated positively by wingless, and negatively by cut in boundary cells. Ectopic Son protein induces wingless and cut expression in wing discs. We hypothesize that there is positive feedback regulation of son by wingless, and negative regulation by cut at the dorsal-ventral boundary during wing development.

Circadian clocks are self-sustained biochemical oscillators. The oscillator of cyanobacteria comprises the products of three kai genes (kaiA, kaiB, and kaiC). The autophosphorylation cycle of KaiC oscillates robustly in the cell with a 24-h period and is essential for the basic timing of the cyanobacterial circadian clock. Recently, period extender (pex), mutants of which show a short period phenotype, was classified as a resetting-related gene. In fact, pex mRNA and the pex protein (Pex) increase during the dark period, and a pex mutant subjected to diurnal light-dark cycles shows a 3-h advance in rhythm phase. Here, we report the x-ray crystallographic analysis and biochemical characterization of Pex from cyanobacterium Synechococcus elongatus PCC 7942. The molecule has an (alpha+beta) structure with a winged-helix motif and is indicated to function as a dimer. The subunit arrangement in the dimer is unique and has not been seen in other winged-helix proteins. Electrophoresis mobility shift assay using a 25-base pair complementary oligonucleotide incorporating the kaiA upstream sequence demonstrates that Pex has an affinity for the double-stranded DNA. Furthermore, mutation analysis shows that Pex uses the wing region to recognize the DNA. The in vivo rhythm assay of Pex shows that the constitutive expression of the pex gene harboring the mutation that fails to bind to DNA lacks the period-prolongation activity in the pex-deficient Synechococcus, suggesting that Pex is a DNA-binding transcription factor.

Transcription factors of the Fox (fork head box) family have been found in all metazoan organisms. They are characterised by an evolutionary conserved DNA-binding domain of winged helix structure. In the South African clawed frog, Xenopus laevis, more than 30 Fox genes have been found so far. This review summarises our present knowledge regarding the general structure and common features of the fork head box and will then characterise Fox genes that have been described in Xenopus. Special attention was paid to the temporal and spatial expression patterns during early embryonic development. For some of these genes, the molecular mechanisms leading to their regulation after the onset of zygotic transcription are known. We also report on functional aspects including target gene regulation, cell or tissue specification and interference with the cell cycle. Finally, Fox proteins serve as mediators of signalling pathways and they might function as checkpoint molecules for the cross-regulatory interactions of different intracellular signal transduction chains.

Determining protein–DNA interactions is important for understanding gene regulation, DNA repair and chromatin structure. Unfortunately, the structures of DNA-bound complexes are often difficult to obtain experimentally, so the development of computational methods that provide good models of these complexes would be valuable. Here, we present a rigid-body docking approach using the computer program DOT. DOT performs a complete, six-dimensional search of all orientations for two rigid molecules and calculates the interaction energy as the sum of electrostatic and van der Waals terms. DOT was applied to three winged-helix transcription factors that share similar DNA-binding structural motifs but bind DNA in different ways. Docking with linear B-form DNA models accomplished several objectives; it (1) distinguished the different ways the transcription factors bind DNA, (2) identified each protein's DNA-binding site and the DNA orientation at the site and (3) gave at least one solution among the three best-ranked that shows the protein side chain–DNA base interactions responsible for recognition. Furthermore, the ensemble of top-ranked, docked linear B-DNA fragments indicated the DNA bending induced upon protein binding. Docking linear B-DNA to structures of the transcription factor FadR suggests that the allosteric, conformational change induced upon effector binding results in loss of the ability to bend DNA as well as loss of sequence-specific interactions with DNA. The electrostatic energy term calculated by DOT is comparable to the electrostatic binding energy calculated by Poisson–Boltzmann methods. Our results show rigid-body docking that includes a rigorous treatment of the electrostatic interaction energy can be effective in predicting protein–DNA interactions. Proteins 2004. © 2004 Wiley-Liss, Inc.

One line of mice harboring a cardiac-specific epoxygenase transgene developed head swelling and rapid neurological decline in young adulthood, and had marked hydrocephalus of the lateral and third ventricles. The transgene was found to be inserted into an intron in the mouse Rfx4 locus. This insertion apparently prevented expression of a novel variant transcript of RFX4 (RFX4_v3), a member of the regulatory factor X family of winged helix transcription factors. Interruption of two alleles resulted in profound failure of dorsal midline brain structure formation and perinatal death,presumably by interfering with expression of downstream genes. Interruption of a single allele prevented formation of the subcommissural organ, a structure important for cerebrospinal fluid flow through the aqueduct of Sylvius, and resulted in congenital hydrocephalus. These data implicate the RFX4_v3 variant transcript as being crucial for early brain development, as well as for the genesis of the subcommissural organ. These findings may be relevant to human congenital hydrocephalus, a birth defect that affects ∼0.6 per 1000 newborns.

Winged helix factors are important regulators of embryonal development and tissue differentiation. They are also involved in translocations found in acute leukemias and solid tumors. We have detected transcripts from five known and four novel winged helix genes in leukemia cell lines and CD34(+) blood progenitor cells by reverse trancription-polymerase chain reaction with degenerate primers on the highly conserved DNA binding domain. The genomic clones coding for two new winged helix proteins, FOXD4a and FOXD4b were isolated by high-stringency hybridization of a human phage library. FOXD4a and FOXD4b are encoded by a 1319 and 1250 bp single exon coding for a winged helix DNA binding domain, an amino-terminal acidic region and a carboxy-terminal proline- and alanine-rich region which correspond to putative transcriptional regulatory motifs. TATA box, CCAAT box, and transcription factor binding motifs have been identified in the 5' region of the genes. In addition, foxD4a and foxD4b cDNA has been isolated from NB-4 mRNA. The fox genes are transcribed in a tissue-restricted pattern in adult and fetal human tissues. FoxD4a and foxD4b mRNA was expressed in the leukemia cell lines KG-1, Kasumi, NB-4, HL-60, U937, THP-1, HEL, U266, Jurkat, and Raji. It has already been shown that winged helix factors are also involved in carcinogenesis. Based upon these studies, our results suggest that FOXD4a and FOXD4b may play a role in leukemogenesis.

The murine Foxc1/Mf1 and Foxc2/Mfh1 genes encode closely related forkhead/winged helix transcription factors with overlapping expression in the forming somites and head mesoderm and endothelial and mesenchymal cells of the developing heart and blood vessels. Embryos lacking either Foxc1 or Foxc2, and most compound heterozygotes, die pre- or perinatally with similar abnormal phenotypes, including defects in the axial skeleton and cardiovascular system. However, somites and major blood vessels do form. This suggested that the genes have similar, dose-dependent functions, and compensate for each other in the early development of the heart, blood vessels, and somites. In support of this hypothesis, we show here that compound Foxc1; Foxc2 homozygotes die earlier and with much more severe defects than single homozygotes alone. Significantly, they have profound abnormalities in the first and second branchial arches, and the early remodeling of blood vessels. Moreover, they show a complete absence of segmented paraxial mesoderm, including anterior somites. Analysis of compound homozygotes shows thatFoxc1 and Foxc2 are both required for transcription in the anterior presomitic mesoderm of paraxis, Mesp1,Mesp2, Hes5, and Notch1, and for the formation of sharp boundaries of Dll1, Lfng, and ephrinB2expression. We propose that the two genes interact with the Notch signaling pathway and are required for the prepatterning of anterior and posterior domains in the presumptive somites through a putative Notch/Delta/Mesp regulatory loop.

Winged helix transcription factors contain two polypeptide loops, or “wings,” that make minor groove contacts with DNA from either side of a three-helix bundle that binds the DNA major groove. While wing 1 is stabilized by a β-sheet, parameters that stabilize wing 2 are unknown. Herein we identify two bulky aromatic residues in wing 2 that stabilize the loop structure and, thereby, the entire protein's DNA binding and transcriptional stimulatory activity by interacting with other residues in the three-helix bundle. Mutations of these wing 2 residues create proteins that are temperature-sensitive for transcriptional activity. Aromatic and/or hydrophobic residues are highly conserved among the 150 known winged helix proteins, suggesting conserved function. We suggest that the winged helix structure evolved by the acquisition of aromatic and/or hydrophobic residues in distal polypeptide sequences that helped stabilize the association of a protein loop (wing 2) with the three-helix bundle, thereby enhancing DNA binding.

Forkhead box protein 1 (FoxA1) is a member of the forkhead family of winged helix transcription factors that plays pivotal roles in the development and differentiation of multiple organs and in the regulation of estrogen-stimulated genes. Conventional analytical methods—electrophoretic mobility shift assay (EMSA) and fluorescence anisotropy (FA)—as well as a gold nanoparticles (AuNPs)-based assay were used to study DNA binding properties of FoxA1 and ligand interruption of FoxA1–DNA binding. In the AuNPs assay, the distinct ability of protein–DNA complex to protect AuNPs against salt-induced aggregation was exploited to screen sequence selectivity and determine the binding affinity constant based on AuNPs color change and absorbance spectrum shift. Both conventional EMSA and FA and the AuNPs assay suggested that FoxA1 binds to DNA in a core sequence-dependent manner and the flanking sequence also played a role to influence the affinity. The EMSA and AuNPs were found to be more sensitive than FA in differentiation of sequence-dependent affinity. With the addition of a spin filtration step, AuNPs assay has been extended for studying small molecular ligand inhibition of FoxA1–DNA interactions enabling drug screening. The results correlate very well with those obtained using FA. ASTAR (Agency for Sci., Tech. and Research, S’pore)

OmpR, a protein that regulates expression of outer membrane porin proteins in enteric bacteria, belongs to a large family of transcription factors. These transcription factors bind DNA and interact productively with RNA polymerase to activate transcription. The two functions, DNA-binding and transcriptional activation, have been localized within the 100 amino acid DNA-binding domain that characterizes members of the OmpR family. Both DNA binding and transcriptional activation by OmpR related proteins have remained poorly understood for lack of structural information or lack of sequence homology with transcription factors of known three-dimensional structure. The recently determined crystal structures of the Escherichia coli OmpR DNA-binding domain (OmpRc) have defined a new subfamily of “winged-helix-turn-helix” DNA-binding proteins. Structural elements of OmpRc can be assigned functional roles by analogy to other winged-helix DNA-binding proteins. A structure based sequence analysis of the OmpR family of transcription factors indicates specific roles for all conserved amino acid residues. Mutagenesis studies performed on several members of this family, OmpR, PhoB, ToxR and VirG, can now be interpreted with respect to the structure.

Cellular differentiation results in transcriptional induction of distinct sets of tissue-specific genes whose expression is required for organ function. Tissue-restricted gene expression relies upon combinatorial interactions of multiple cis-acting DNA sequences bound by families of cell-specific nuclear factors (1). One of these regulatory families is represented by the hepatocyte nuclear factor-3 (HNF-3α and β) proteins (2), which mediate the transcription of liver (3) and lung (4–7) specific genes. The HNF-3 proteins bind DNA as a monomer via a homologous winged helix DNA-binding domain (8). Mammalian HNF-3 and Drosophila homeotic fork head (fkh) (9) proteins were the first identified members of a large family of transcription factors that shares homology in the winged helix DNA-binding domain and is involved in differentiation of diverse cellular lineages (3). Accumulating evidence demonstrates that the winged helix transcription factors are involved in cellular differentiation during embryonic development and organogenesis. The HNF-3α and HNF-3β genes are expressed during the primitive streak stage of mouse embryogenesis (10–12). Targeted disruption of the HNF-3β gene causes an embryonic lethal phenotype that exhibits defects in the formation of notochord, neurotube, somites, and gut endoderm (13, 14). Targeted disruption of other winged helix family members, brain factor-1 and brain factor-2, demonstrates an involvement in morphogenesis of the cerebral hemispheres and in branching of the ureter and renal collecting system respectively (15, 16). Disruption of a winged-helix gene (whn) is responsible for the phenotype of the nude mouse mutation (17). Furthermore, aberrant expression of altered winged helix proteins has also been associated with neoplastic transformations (18–20). In a previous study we isolated a full-length mouse HNF-3/fkh homolog-4 (HFH-4) cDNA, a winged helix family member encoding a 421 amino acid polypeptide containing several putative transcriptional activation motifs (5). In situ hybridization studies of adult rodent lung showed that the winged helix family members HFH-4 and HNF-3α are coexpressed in the proximal bronchiolar epithelium (5). HFH-4 initiates expression in the proximal bronchial epithelium of embryonic lung at 14.5 day post coitum (p.c.) (21). In this study, we report on a novel expression pattern of the HFH-4 gene in the presumptive choroid plexus epithelium of the mouse embryo and show that its expression continues during the differentiation of the choroid plexus epithelium. We determine the HFH-4 DNA-binding consensus sequence and show that HFH-4 is a potent transcriptional activator. We use the HFH-4 DNA-binding consensus sequence to identify putative target genes in the choroid plexus and bronchiolar epithelium.

The BirA biotin protein ligase of Escherichia coli belongs to the winged helix-turn-helix (wHTH) family of transcriptional regulators. The N-terminal BirA domain is required for both transcriptional regulation of biotin synthesis and biotin protein ligase activity. We addressed the structural and functional role of the wing of the wHTH motif in both BirA functions. A panel of N-terminal deletion mutant proteins including a discrete deletion of the wing motif were unable to bind DNA. However, all the N-terminal deletion mutants weakly complemented growth of a ΔbirA strain at low biotin concentrations, indicating compromised ligase activity. A wing domain chimera was constructed by replacing the BirA wing with the nearly isosteric wing of the E. coli OmpR transcription factor. Although this chimera BirA was defective in operator binding, it was much more efficient in complementation of a ΔbirA strain than was the wing-less protein. The enzymatic activities of the wing deletion and chimera proteins in the in vitro synthesis of biotinoyl-5′-AMP differed greatly. The wing deletion BirA accumulated an off pathway compound, ADP, whereas the chimera protein did not. Finally, we report that a single residue alteration in the wing bypasses the deleterious effects caused by mutations in the biotin-binding loop of the ligase active site. We believe that the role of the wing in the BirA enzymatic reaction is to orient the active site and thereby protect biotinoyl-5′-AMP from attack by solvent. This is the first evidence that the wing domain of a wHTH protein can play an important role in enzymatic activity.

BldD regulates transcription of key developmental genes in Streptomyces coelicolor. While the N-terminal domain is responsible for both dimerization and DNA binding, the structural and functional roles of the C-terminal domain (CTD) remain largely unexplored. Here, the solution structure of the BldD-CTD shows a novel winged-helix domain fold not compatible with DNA binding, due to the negatively charged surface and presence of an additional helix. Meanwhile, a small elongated groove with conserved hydrophobic patches surrounded by charged residues suggests that the BldD-CTD could be involved in protein-protein interactions that provide transcriptional regulation.

The human nuclear factor related to kappa-B-binding protein (NFRKB) is a 1299-residue protein that is a component of the metazoan INO80 complex involved in chromatin remodeling, transcription regulation, DNA replication and DNA repair. Although full length NFRKB is predicted to be around 65% disordered, comparative sequence analysis identified several potentially structured sections in the N-terminal region of the protein. These regions were targeted for crystallographic studies, and the structure of one of these regions spanning residues 370-495 was determined using the JCSG high-throughput structure determination pipeline. The structure reveals a novel, mostly helical domain reminiscent of the winged-helix fold typically involved in DNA binding. However, further analysis shows that this domain does not bind DNA, suggesting it may belong to a small group of winged-helix domains involved in protein-protein interactions. © 2012 Kumar et al.

The transcription factor neurogenin 3 (Neurog3 or Ngn3) controls islet cell fate specification in multipotent pancreatic progenitor cells in the mouse embryo. However, our knowledge of the genetic programs implemented by Ngn3, which control generic and islet subtype-specific properties, is still fragmentary. Gene expression profiling in isolated Ngn3-positive progenitor cells resulted in the identification of the uncharacterized winged helix transcription factor Rfx6. Rfx6 is initially expressed broadly in the gut endoderm, notably in Pdx1-positive cells in the developing pancreatic buds, and then becomes progressively restricted to the endocrine lineage, suggesting a dual function in both endoderm development and islet cell differentiation. Rfx6 is found in postmitotic islet progenitor cells in the embryo and is maintained in all developing and adult islet cell types. Rfx6 is dependent on Ngn3 and acts upstream of or in parallel with NeuroD, Pax4 and Arx transcription factors during islet cell differentiation. In zebrafish, the Rfx6 ortholog is similarly found in progenitors and hormone expressing cells of the islet lineage. Loss-of-function studies in zebrafish revealed that rfx6 is required for the differentiation of glucagon-, ghrelin- and somatostatin-expressing cells, which, in the absence of rfx6, are blocked at the progenitor stage. By contrast, beta cells, whose number is only slightly reduced, were no longer clustered in a compact islet. These data unveil Rfx6 as a novel regulator of islet cell development.

Two winged-helix transcription factors, FoxG1 (previously called chick brain factor1, CBF1) and FoxD1 (chick brain factor2, CBF2), are expressed specifically in the nasal and temporal regions of the developing chick retina, respectively. We previously demonstrated that FoxG1 controls the expression of topographic molecules including FoxD1, and determines the regional specificity of the nasal retina. FoxD1 is known to prescribe temporal specificity, however, molecular mechanisms and downstream targets have not been elucidated. Here we addressed the genetic mechanisms for establishing temporal specificity in the developing retina using an in ovo electroporation technique. Fibroblast growth factor (Fgf) and Wnt first play pivotal roles in inducing the region-specific expression of FoxG1 and FoxD1 in the optic vesicle. Misexpression of FoxD1 represses the expression of FoxG1, GH6, SOHo1, and ephrin-A5, and induces that of EphA3 in the retina. GH6 and SOHo1 repress the expression of FoxD1. In contrast to the inhibitory effect of FoxG1 on bone morphogenic protein (BMP) signaling, FoxD1 does not alter the expression of BMP4 or BMP2. Studies with chimeric mutants of FoxD1 showed that FoxD1 acts as a transcription repressor in controlling its downstream targets in the retina. Taken together with previous findings, our data suggest that FoxG1 and FoxD1 are located at the top of the gene cascade for regional specification along the nasotemporal (anteroposterior) axis in the retina, and FoxD1 determines temporal specificity.

Human KIN17 is a 45-kDa eukaryotic DNA- and RNA-binding protein that plays an important role in nuclear metabolism and in particular in the general response to genotoxics. Its amino acids sequence contains a zinc finger motif (residues 28-50) within a 30-kDa N-terminal region conserved from yeast to human, and a 15-kDa C-terminal tandem of SH3-like subdomains (residues 268-393) only found in higher eukaryotes. Here we report the solution structure of the region 51-160 of human KIN17. We show that this fragment folds into a three-alpha-helix bundle packed against a three-stranded beta-sheet. It belongs to the winged helix (WH) family. Structural comparison with analogous WH domains reveals that KIN17 WH module presents an additional and highly conserved 3(10)-helix. Moreover, KIN17 WH helix H3 is not positively charged as in classical DNA-binding WH domains. Thus, human KIN17 region 51-160 might rather be involved in protein-protein interaction through its conserved surface centered on the 3(10)-helix.

CopR of Lactococcus lactis is a copper-responsive repressor involved in copper homoeostasis. It controls the expression of a total of 11 genes, the CopR regulon, in a copper-dependent manner. In the absence of copper, CopR binds to the promoters of the CopR regulon. Copper releases CopR from the promoters, allowing transcription of the downstream genes to proceed. CopR binds through its N-terminal domain to a ‘cop box’ of consensus TACANNTGTA, which is conserved in Firmicutes. We have solved the NMR solution structure of the N-terminal DNA-binding domain of CopR. The protein fold has a winged helix structure resembling that of the BlaI repressor which regulates antibiotic resistance in Bacillus licheniformis. CopR differs from other copper-responsive repressors, and the present structure represents a novel family of copper regulators, which we propose to call the CopY family.

Microbial genome sequencing projects have revealed an apparently wide distribution of SmtB/ArsR metal-responsive transcriptional regulators among prokaryotes. Using a position-dependent weight matrix approach, prokaryotic genome sequences were screened for SmtB/ArsR DNA binding sites using data derived from intergenic sequences upstream of orthologous genes encoding these regulators. Sixty SmtB/ArsR operators linked to metal detoxification genes, including nine among various archaeal species, are predicted among 230 annotated and draft prokaryotic genome sequences. Independent multiple sequence alignments of putative operator sites and corresponding winged helix-turn-helix motifs define sequence signatures for the DNA binding activity of this SmtB/ArsR subfamily. Prediction of an archaeal SmtB/ArsR based upon these signature sequences is confirmed using purified Methanosarcina acetivorans C2A protein and electrophoretic mobility shift assays. Tools used in this study have been incorporated into a web application, the Prokaryotic InterGenic Exploration Database (PIGED; http://bioinformatics.uwp.edu/~PIGED/home.htm), facilitating comparable studies. Use of this tool and establishment of orthology based on DNA binding signatures holds promise for deciphering potential cellular roles of various archaeal winged helix-turn-helix transcriptional regulators.

MAN1 is an integral protein of the inner nuclear membrane that interacts with nuclear lamins and emerin, thus playing a role in nuclear organization. It also binds to chromatin-associated proteins and transcriptional regulators, including the R-Smads, Smad1, Smad2, and Smad3. Mutations in the human gene encoding MAN1 cause sclerosing bone dysplasias, which sometimes have associated skin abnormalities. At the molecular level, these mutations lead to loss of the MAN1-R-Smads interaction, thus perturbing transforming growth factor beta superfamily signaling pathway. As a first step to understanding the physical basis of MAN1 interaction with R-Smads, we here report the structural characterization of the carboxyl-terminal nucleoplasmic region of MAN1, which is responsible for Smad binding. This region exhibits an amino-terminal globular domain adopting a winged helix fold, as found in several Smad-associated sequence-specific DNA binding factors. Consistently, it binds to DNA through the positively charged recognition helix H3 of its winged helix motif. However, it does not show the predicted carboxyl-terminal U2AF homology domain in solution, suggesting that the folding and stability of such a domain in MAN1 depend upon binding to an unidentified partner. Modeling the complex between DNA and the winged helix domain shows that the regions involved in DNA binding are essentially distinct from those reported to be involved in Smad binding. This suggests that MAN1 binds simultaneously to R-Smads and their targeted DNA sequences.

Response regulators are the output component of two-component regulatory systems, the predominant form of signal transduction systems utilized by prokaryotes. The majority of response regulators function as transcription factors, yet detailed descriptions of their mechanisms of DNA binding and its consequences are lacking. Versatility in the modes of DNA binding is evident with winged helix-turn-helix proteins, raising doubts that mechanisms of DNA binding will be generalizable among members of the family. The current focus of some of the research efforts aimed at understanding activation and DNA binding by response regulators is highlighted in this review.

We have investigated the regulation of the activin-inducible distal element (DE) of the Xenopus goosecoid promoter. The results show that paired-like homeodomain transcription factors of the Mix family, Mixer and Milk, but not Mix.1, mediate activin/TGF-β-induced transcription through the DE by interacting with the effector domain of Smad2, thereby recruiting active Smad2/Smad4 complexes to the Mixer/Milk-binding site. We identify a short motif in the carboxyl termini of Mixer and Milk, which is demonstrated to be both necessary and sufficient for interaction with the effector domain of Smad2 and is required for mediating activin/TGF-β-induced transcription. This motif is not confined to these homeodomain proteins, but is also present in the Smad2-interacting winged-helix proteins Xenopus Fast-1, human Fast-1, and mouse Fast-2. We demonstrate directly that transcription factors of different DNA-binding specificity recruit activated Smads to distinct promoter elements via a common mechanism. These observations, together with the temporal and spatial expression patterns ofMixer and Milk, lead us to propose a model for mesoendoderm formation in Xenopus in which these homeodomain transcription factor/Smad complexes play a role in initiating and maintaining transcription of target genes in response to endogenous activin-like signals.

It has been shown that topographic expression of two winged-helix transcription factors, CBF1/c-qin and CBF2, and a receptor tyrosine kinase EphA3 (Mek4/Cek4) play important roles in establishing the topographic retinotectal projection map along the rostrocaudal axis. The interrelationship among these topographic molecules in the chick retina was studied during development. The topographic expression of CBF1 and CBF2 preluded the graded expression of EphA3, but their precise expression profiles did not exactly fit together. However, interestingly, CBF1 and CBF2 were properly expressed, together with EphA3, in immortalized cell lines derived from the quail retina, which maintained position-specific characteristics. The expression of another topographic molecule SOHo-1, the sensory organ homeobox-1 transcription factor, was separate from EphA3 expression. Ectopic expression of CBF1 using in ovo electroporation repressed the expression of CBF2, and misexpression of CBF2 influenced the graded localization of EphA3 in the retina, albeit imperfectly. Taken together, it is suggested that retinal cells first begin to express CBF1 or CBF2 according to their topographic positions, generate cellular descendants in which the expression of CBF1 and CBF2 is maintained cell-autonomously, and then establish the nasotemporal gradient of EphA3 under the control of CBF2, although indirect.

The retroviral oncogene qin codes for a protein that belongs to the family of the winged helix transcription factors. The viral Qin protein, v-Qin, differs from its cellular counterpart, c-Qin, by functioning as a stronger transcriptional repressor and a more efficient inducer of tumors. This observation suggests that repression may be important in tumorigenesis. To test this possibility, chimeric proteins were constructed in which the Qin DNA-binding domain was fused to either a strong repressor domain (derived from the Drosophila Engrailed protein) or a strong activator domain (from the herpes simplex virus VP16 protein). The chimeric transcriptional repressor, Qin–Engrailed, transformed chicken embryo fibroblasts in culture and induced sarcomas in young chickens. The chimeric activator, Qin–VP16, failed to transform cells in vitro or in vivo and caused cellular resistance to oncogenic transformation by Qin. These data support the conclusion that the Qin protein induces oncogenic transformation by repressing the transcription of genes which function as negative growth regulators or tumor suppressors.

The human HSPC280 protein belongs to a new family of low molecular weight proteins, which is only present in eukaryotes, and is absent in fungi. The solution structure of HSPC280 was determined using multidimensional NMR spectroscopy. The overall structure consists of three α-helices and four antiparallel β-strands and has a winged helix-like fold. However, HEPC280 is not a typical DNA-binding winged helix protein in that it lacks DNA-binding activity. Unlike most winged-helix proteins, HSPC280 has an unusually long 13-residue (P62-V74) wing 1 loop connecting the β3 and β4 strands of the protein. Molecules of HSPC280 have a positively charged surface on one side and a negatively charged surface on the other side of the protein structure. Comparisons with the C-terminal 80-residue domain of proteins in the Abra family reveal a conserved hydrophobic groove in the HSPC280 family, which may allow HSPC280 to interact with other proteins.

The murine Mf1 and Mfh1 genes have overlapping patterns of expression in the embryo and encode forkhead/winged helix transcription factors with virtually identical DNA binding domains. Previous studies have shown that Mfh1 null mutants have severe cardiovascular defects, including interruptions and coarctations of the aortic arch and ventricular septal defects (Iida et al., Development 124, 4627–4638, 1997). Here, we show that Mf1lacZ homozygous null mutants also have a similar spectrum of cardiovascular abnormalities. Moreover, most embryos doubly heterozygous for Mfh1tm1 and Mf1lacZ die before birth with interruptions and coarctations of the aortic arch, dysgenesis of the aortic and pulmonary valves, ventricular septal defects, and other cardiac anomalies. This nonallelic noncomplementation and the similar patterns of expression of the two genes in the mesenchyme and endothelial cells of the branchial arches, outflow tract, and heart suggest thatMf1 and Mfh1 play interactive roles in the morphogenesis of the cardiovascular system. Implications for the development of human congenital heart defects are discussed.