Family Of DNA-binding Proteins Research Articles

The plant-specific family of DNA-binding proteins containing three HMG-box domains interacts with mitotic and meiotic chromosomes

• The high mobility group (HMG)-box represents a DNA-binding domain that is found in various eukaryotic DNA-interacting proteins. Proteins that contain three copies of the HMG-box domain, termed 3 × HMG-box proteins, appear to be specific to plants. The Arabidopsis genome encodes two 3 × HMG-box proteins that were studied here. • DNA interactions were examined using electrophoretic mobility shift assays, whereas expression, subcellular localization and chromosome association were mainly analysed by different types of fluorescence microscopy. • The 3 × HMG-box proteins bind structure specifically to DNA, display DNA bending activity and, in addition to the three HMG-box domains, the basic N-terminal domain contributes to DNA binding. The expression of the two Arabidopsis genes encoding 3 × HMG-box proteins is linked to cell proliferation. In synchronized cells, expression is cell cycle dependent and peaks in cells undergoing mitosis. 3 × HMG-box proteins are excluded from the nuclei of interphase cells and localize to the cytosol, but, during mitosis, they associate with condensed chromosomes. The 3 × HMG-box2 protein generally associates with mitotic chromosomes, while 3 × HMG-box1 is detected specifically at 45S rDNA loci. • In addition to mitotic chromosomes the 3 × HMG-box proteins associate with meiotic chromosomes, suggesting that they are involved in a general process of chromosome function related to cell division, such as chromosome condensation and/or segregation.

Increased vegetative development and sturdiness of storekeeper-transgenic tobacco

Abstract The STOREKEEPER (STK) family of DNA-binding proteins work as transcription factors and the ectopic expression of two stk-like genes from Arabidopsis thaliana, stk01 (At1g61730) and stk03 (At4g00238), in tobacco increased the number of vegetative internodes and promoted plant and leaf size, stem diameter and sturdiness. The development of these plants started with rosette formation while pronounced shoot elongation and flowering was delayed. Moreover, when the STK01 and STK03 proteins were fused to the Herpes Simplex Virus VP16 transcriptional activation domain and expressed in tobacco the vigorous storekeeper-phenotype did not appear indicating that transgenic STK-like proteins in part worked as repressors of tobacco reproductive development. Furthermore, Yeast Two-Hybrid screenings proved that STK01 and STK03 can form homodimers and heterodimers with further members of the STKlike family. Therefore, we assume that interactions between transgenic Arabidopsis STKs and resident tobacco STKs could have contributed to the observed developmental changes in transgenic tobacco. Our findings open up promising applications for overexpression of stk-like genes in crops that benefit from increased sturdiness and vegetative organ development, such as tobacco in molecular farming approaches, biomass-based energy crops and medicinal plants that produce bioactive compounds in leaves.

Abstract 999: PTEN/PI-3 kinase pathway's regulation of β-catenin in epithelial to mesenchymal transition (EMT)

Abstract INTRODUCTION: Cancer metastasis is responsible for 90% of cancer-related deaths. For metastasis to occur, cells must shed their epithelial phenotype and acquire a mesenchymal phenotype in order to gain the characteristic motility and invasiveness. These alterations are referred to as “Epithelial- Mesenchymal Transition (EMT)”. Beta-Catenin (β-cat) is a dual-role protein. It serves a role in cell-cell adhesion; it links E-cadherin to the actin cytoskeleton. The second role is its involvement in the canonical Wnt-signaling pathway. It acts as a co-activator of the lymphoid enhancer factor/ T-cell factor family of DNA-binding proteins. The binding of this complex activates transcription of genes that control cell proliferation and invasiveness. Excessive transcription of these genes mediated by excess β-cat is associated with the oncogenic properties of cancer cells and β-cat has been widely implicated as an oncogene in human cancers. We determined the role of β-cat and the regulation of its expression and activity by the PTEN/ Phosphatidyl-inositol-3 Kinase (PI3K) pathway during EMT associated with melanoma progression. PTEN is a dual lipid/protein phosphatase which functions to oppose the kinase function of PI3K. Absence of PTEN allows for the deregulation of the pathway, leading to sustenance of pro-survival and anti-apoptotic cellular response. METHODS: Our studies were done using a panel of cell lines representative of the various phases of melanoma progression as a model of EMT (Melanocyte=HeMaLp; Mixed Radial & Vertical Growth Phase = A375; Radial Growth Phase = WM35; Vertical Growth Phase = WM793; Metastatic Melanoma = A2058). We determined alterations in cellular expression, sub cellular distribution and activity of β -Cat, and PTEN during EMT progression. RESULTS: We determined that there was a loss in the expression of the tumor suppressor PTEN in the melanoma cell lines with complete absence of its expression in the vertical and metastatic melanoma cell lines. This was correlated with an increase in total cellular levels of β-Cat and active β-Cat. We then carried out the transient transfection of the PTEN-null metastatic melanoma cell line (A2058) with a vector containing wild type PTEN tagged with GFP. Our results show a decrease in overall β-Cat and active-β-Cat levels. There was an increase in phospho-β-Cat at ser-33/37 and thr-41 without any alteration to the phosphorylation at ser-45. These changes are associated with a decrease in cellular levels of β-Cat with a significant attenuation of nuclear levels of active β-Cat. CONCLUSIONS: Our results show a direct regulatory role of PTEN/PI3K pathway upon the levels and activity of β-Cat. SIGNIFICANCE: Components of the PTEN/PI3-Kinase pathway involved in regulating β-Cat levels and activity represent potential molecular targets, which could be intercepted to limit progression to metastatic disease. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 999. doi:10.1158/1538-7445.AM2011-999

The pipsqueak-domain proteins Distal antenna and Distal antenna-related restrict Hunchback neuroblast expression and early-born neuronal identity

A fundamental question in brain development is how precursor cells generate a diverse group of neural progeny in an ordered manner. Drosophila neuroblasts sequentially express the transcription factors Hunchback (Hb), Krüppel (Kr), Pdm1/Pdm2 (Pdm) and Castor (Cas). Hb is necessary and sufficient to specify early-born temporal identity and, thus, Hb downregulation is essential for specification of later-born progeny. Here, we show that distal antenna (dan) and distal antenna-related (danr), encoding pipsqueak motif DNA-binding domain protein family members, are detected in all neuroblasts during the Hb-to-Cas expression window. Dan and Danr are required for timely downregulation of Hb in neuroblasts and for limiting the number of early-born neurons. Dan and Danr function independently of Seven-up (Svp), an orphan nuclear receptor known to repress Hb expression in neuroblasts, because Dan, Danr and Svp do not regulate each other and dan danr svp triple mutants have increased early-born neurons compared with either dan danr or svp mutants. Interestingly, misexpression of Hb can induce Dan and Svp expression in neuroblasts, suggesting that Hb might activate a negative feedback loop to limit its own expression. We conclude that Dan/Danr and Svp act in parallel pathways to limit Hb expression and allow neuroblasts to transition from making early-born neurons to late-born neurons at the proper time.

HU Induced Perturbation to the Structure and Dynamics of a Flexible DNA Substrate

The structure and dynamics of the bacterial chromosome are maintained by many proteins. One of the most abundant proteins, a member of the DNABII family of DNA-binding proteins, is HU (Heat_Unstable). HU, an architectural protein introduces sharp bends of 120-160 degrees into DNA upon binding. The DNA bending induced by these proteins is important for transcriptional regulation, initiation of replication, Mu transposition, base excision repair, recombination, and negative supercoiling in bacteria. HU exhibits a strong preference for distorted or kinked DNA and binds with high affinity to nicks, gaps, cruciform, and sticky ends. Little structural or dynamic information is available regarding the perturbation of these DNA motifs upon HU binding; although they all contain a flexible junction. Increased understanding of HU binding to these motifs would illuminate the nature of HU regulation of DNA structure. This information also gives insight into the general mode of recognition and binding for all non-sequence-specific DNA binding proteins found in both prokaryotes and eukaryotes. We have employed several fluorescence spectroscopic techniques to address the nature of the HU-DNA binding interaction. Using fluorescence anisotropy measurements, we have determined the dissociation constant in solution for HU binding to 3’overhang DNA substrate to be 3.41E-09+/- 1.2E-09 M, which is in good agreement with literature results. The stoichiometry for the specific binding of HU to these substrates is one to one, while non-specific binding leads to higher order complexes. Preliminary fluorescence resonance energy transfer (FRET) results suggest bending of the DNA substrate upon HU binding. Further information about the mechanism of HU-induced bending, structural recognition and binding is obtained through the use of FRET mapping, time-resolved fluorescence spectroscopy, and stopped-flow kinetic methods.

Tracing the Origin of the Fungal α1 Domain Places Its Ancestor in the HMG-Box Superfamily: Implication for Fungal Mating-Type Evolution

BackgroundFungal mating types in self-incompatible Pezizomycotina are specified by one of two alternate sequences occupying the same locus on corresponding chromosomes. One sequence is characterized by a gene encoding an HMG protein, while the hallmark of the other is a gene encoding a protein with an α1 domain showing similarity to the Matα1p protein of Saccharomyces cerevisiae. DNA-binding HMG proteins are ubiquitous and well characterized. In contrast, α1 domain proteins have limited distribution and their evolutionary origin is obscure, precluding a complete understanding of mating-type evolution in Ascomycota. Although much work has focused on the role of the S. cerevisiae Matα1p protein as a transcription factor, it has not yet been placed in any of the large families of sequence-specific DNA-binding proteins.Methodology/Principal FindingsWe present sequence comparisons, phylogenetic analyses, and in silico predictions of secondary and tertiary structures, which support our hypothesis that the α1 domain is related to the HMG domain. We have also characterized a new conserved motif in α1 proteins of Pezizomycotina. This motif is immediately adjacent to and downstream of the α1 domain and consists of a core sequence Y-[LMIF]-x(3)-G-[WL] embedded in a larger conserved motif.Conclusions/SignificanceOur data suggest that extant α1-box genes originated from an ancestral HMG gene, which confirms the current model of mating-type evolution within the fungal kingdom. We propose to incorporate α1 proteins in a new subclass of HMG proteins termed MATα_HMG.

Transcriptional Regulation of γ-Globin Gene Expression by KLF4

AbstractAbstract 645Kruppel-like factors (KLFs) are a family of Cys2His2 zinc-finger DNA binding proteins that regulate gene expression through CACCC/GC/GT box binding in various gene promoters. The CACCC element is also critical for developmental regulation of the human γ-globin and β-globin genes; therefore studies to identify transcription factors that bind the CACCC element to alter gene expression are desirable. By microarray-based gene profiling, we identified two Kruppel-like factors, KLF4 and KLF12 whose expression levels decreased simultaneously with γ-globin silencing during in vitro erythroid maturation. Subsequent reverse transcription quantitative PCR (RT-qPCR) analysis confirmed KLF4 and KLF12 mRNA levels decreased 56-fold and 16-fold respectively in erythroid progenitors from day 7 to day 28 with over 90% γ-globin gene silencing. The effects of known fetal hemoglobin inducers hemin (50μM) and sodium butyrate (2mM) on KLF factor expression was tested in K562 cells. Hemin and sodium butyrate increased KLF4 3-fold (p<0.05) and 13-fold (p<0.01) respectively while KLF12 was only induced by butyrate. Likewise, hemin treatment of KU812 leukemia cells, which actively express γ-globin and β-globin, produced a 7-fold increase in KLF4 (p<0.05) while KLF12 levels were not changed suggesting KLF4 may be directly involved in γ-globin gene regulation. To characterize its role further siRNA-mediated loss of function studies were performed in K562 cells. A 60% knockdown of KLF4 expression produced 40% attenuation of γ-globin transcription (p<0.05). To confirm this effect, rescue experiments were performed as follows: K562 cells were treated with 100nM siKLF4 alone or in combination with the pMT3-KLF4 expression vector (10 and 20μg) for 48 hrs. The 40% knockdown of γ-globin expression produced by siKLF4 was rescued to baseline levels after enforced pMT3-KLF4 expression (p<0.05). To establish whether KLF4 directly stimulates γ-globin promoter activity, we performed co-transfection of pMT3-KLF4 and the Gγ-promoter (-1500 to +36) cloned into the pGL4.17 Luc2/neo vector; a dose-dependent increase in luciferase activity (2- to 5-fold; p<0.001) was observed. Furthermore, enforced expression of pMT3-KLF4 augmented endogenous γ-globin expression 2-fold (p<0.01). Collectively, these studies suggest that KLF4 acts as a trans-activator of γ-globin gene transcription. To address the physiological relevance of these findings, studies were extended to human primary erythroid cells grown in a two-phase liquid culture system. At day 11 when γ-globin gene expression was maximal, siKLF4 treatment produced a 60% decrease in γ/β-globin mRNA levels (p<0.001). By contrast, enforced pMT3-KLF4 expression enhanced γ/β-globin 1.5-fold at day 11 and day 28 (after γ-globin silencing); HbF levels were induced 1.5-fold (p<0.05) which was demonstrated by enzyme-linked immunosorbent assay. To gain insights into the molecular mechanism of KLF4-mediated γ-globin regulation, electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation assay (ChIP) were completed. Since CREB binding protein (CBP) is known to function as a co-activator for KLF1, 4 and 13, we also tested its role in γ-globin gene regulation. EMSA performed with K562 nuclear extract and a [γ-32P] labeled γ-CACC probe (-155 to -132 relative to the γ-globin cap site) produced three DNA-protein complexes; the addition of KLF4 or CBP antibody resulted in a marked decrease in intensity of all complexes suggesting these factors bind the γ-CACC element. ChIP assay demonstrated 10-fold and 20-fold chromatin enrichment with KLF4 and CBP antibody respectively (p<0.001) confirming in vivo binding at the γ-CACC region. Lastly, co-immunoprecipitation established protein-protein interaction between KLF4 and CBP in K562 cells. Future studies will investigate the role of CBP in KLF4-mediated γ-globin regulation which will provide molecular targets for fetal hemoglobin induction and treatment of sickle cell anemia and β-thalassemia. Disclosures:No relevant conflicts of interest to declare.

Aryl Hydrocarbon Receptor-Null Allele Mice Have Hematopoietic Stem/Progenitor Cells with Abnormal Characteristics and Functions

The aryl hydrocarbon receptor (AhR) belongs to the basic helix-loop-helix family of DNA-binding proteins that play a role in the toxicity and carcinogenicity of certain chemicals. The most potent ligand of the AhR known is 2,3,7,8-tetracholorodibenzo-p-dioxin. We previously reported tetrachlorodibenzo-p-dioxin-induced alterations in numbers and function of hematopoietic stem cells (HSCs). To better understand a possible role of the AhR in hematopoiesis, studies were undertaken in young adult AhR null-allele (KO) mice. These mice have enlarged spleens with increased number of cells from different lineages. Altered expression of several chemokine, cytokine, and their receptor genes were observed in spleen. The KO mice have altered numbers of circulating red and white blood cells, as well as a circadian rhythm-associated 2-fold increase in the number of HSC-enriched Lin(-)Sca-1(+)c-Kit(+) (LSK) cells in bone marrow. Primary cultures of KO HSCs and in vivo bromodeoxyuridine incorporation studies demonstrated an approximate 2-fold increased proliferative ability of these cells. More LSK cells from KO mice were in G(1) and S phases of cell cycle. Competitive repopulation studies also indicated significant functional changes in KO HSCs. LSK cells showed increased expression of Cebpe and decreased expression of several hematopoiesis-associated genes. These data indicate that AhR has a physiological and functional role in hematopoiesis. The AhR appears to play a role in maintaining the normal quiescence of HSCs.

Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria Parasite

The molecular mechanisms underlying transcriptional regulation in apicomplexan parasites remain poorly understood. Recently, the Apicomplexan AP2 (ApiAP2) family of DNA binding proteins was identified as a major class of transcriptional regulators that are found across all Apicomplexa. To gain insight into the regulatory role of these proteins in the malaria parasite, we have comprehensively surveyed the DNA-binding specificities of all 27 members of the ApiAP2 protein family from Plasmodium falciparum revealing unique binding preferences for the majority of these DNA binding proteins. In addition to high affinity primary motif interactions, we also observe interactions with secondary motifs. The ability of a number of ApiAP2 proteins to bind multiple, distinct motifs significantly increases the potential complexity of the transcriptional regulatory networks governed by the ApiAP2 family. Using these newly identified sequence motifs, we infer the trans-factors associated with previously reported plasmodial cis-elements and provide evidence that ApiAP2 proteins modulate key regulatory decisions at all stages of parasite development. Our results offer a detailed view of ApiAP2 DNA binding specificity and take the first step toward inferring comprehensive gene regulatory networks for P. falciparum.

Insights into the folding pathway of the Engrailed Homeodomain protein using replica exchange molecular dynamics simulations

Protein folding studies were carried out by performing microsecond time scale simulations on the ultrafast/fast folding protein Engrailed Homeodomain (EnHD) from Drosophila melanogaster. It is a three-helix bundle protein consisting of 54 residues (PDB ID: 1ENH). The positions of the helices are 8–20 (Helix I), 26–36 (Helix II) and 40–53 (Helix III). The second and third helices together form a Helix-Turn-Helix (HTH) motif which belongs to the family of DNA binding proteins. The molecular dynamics (MD) simulations were performed using replica exchange molecular dynamics (REMD). REMD is a method that involves simulating a protein at different temperatures and performing exchanges at regular time intervals. These exchanges were accepted or rejected based on the Metropolis criterion. REMD was performed using the AMBER FF03 force field with the generalised Born solvation model for the temperature range 286–373 K involving 30 replicas. The extended conformation of the protein was used as the starting structure. A simulation of 600 ns per replica was performed resulting in an overall simulation time of 18 μs. The protein was seen to fold close to the native state with backbone root mean square deviation (RMSD) of 3.16 Å. In this low RMSD structure, the Helix I was partially formed with a backbone RMSD of 3.37 Å while HTH motif had an RMSD of 1.81 Å. Analysis suggests that EnHD folds to its native structure via an intermediate in which the HTH motif is formed. The secondary structure development occurs first followed by tertiary packing. The results were in good agreement with the experimental findings.

Control of salicylic acid synthesis and systemic acquired resistance by two members of a plant-specific family of transcription factors

Salicylic acid (SA) is a defense hormone required for both local and systemic acquired resistance (SAR) in plants. Pathogen infections induce SA synthesis through up-regulating the expression of Isochorismate Synthase 1 (ICS1), which encodes a key enzyme in SA production. Here we report that both SAR Deficient 1 (SARD1) and CBP60g are key regulators for ICS1 induction and SA synthesis. Whereas knocking out SARD1 compromises basal resistance and SAR, overexpression of SARD1 constitutively activates defense responses. In the sard1-1 cbp60g-1 double mutant, pathogen-induced ICS1 up-regulation and SA synthesis are blocked in both local and systemic leaves, resulting in compromised basal resistance and loss of SAR. Electrophoretic mobility shift assays showed that SARD1 and CBP60g represent a plant-specific family of DNA-binding proteins. Both proteins are recruited to the promoter of ICS1 in response to pathogen infections, suggesting that they control SA synthesis by regulating ICS1 at the transcriptional level.

Isolation and characterization of two Medicago falcate AP2/EREBP family transcription factor cDNA, MfDREB1 and MfDREB1s

DREB transcription factors play an important role in tolerance to abiotic stress in high plants. In this work, two new DRE-binding protein genes MfDREB1 and MfDREB1s cDNA that encoded an AP2/EREBP type transcription factor were isolated by RT-PCR from Medicago falcate seedlings. Sequence analysis showed MfDREB1 and MfDREB1s were almost identical except that there was a 202bp fragment at the 3' end of the MfDREB1s cDNA that is absent in MfDREB1 cDNA. The MfDREB1 has a open reading frame of 651bp, which encodes 216 amino acid residues. The putative protein is deduced a predicted molecular mass of 24.6kDa and a pI of 5.95. The MfDREB1s has a open reading frame of 555bp, the putative protein is 184 amino acid long with a predicted molecular weight of 20.8kDa, pI 9.11. The Protein Blast data revealed that the two proteins can be classified as a typical member of the AP2/EREBP family of DNA-binding proteins. The comparison of the MfDREB1 cDNA and MfDREB1s cDNA with their corresponding genes in genomic DNAshowed that the size and nucleotide sequence of the cDNA was identical to that of the genomic DNA. This suggested that the genomic MfDREB1 gene and MfDREB1s gene had no introns. Southern blot analysis indicated that MfDREB1 and MfDREB1s are multi-copy genes in Medicago falcate genome. Northern blot analysis indicated that the MfDREB1 and MfDREB1s genes were induced by low temperature stress.

Distinct class of DNA-binding domains is exemplified by a master regulator of phenotypic switching in Candida albicans.

Among the most important classes of regulatory proteins are the sequence-specific DNA-binding proteins that control transcription through the occupancy of discrete DNA sequences within genomes. Currently, this class of proteins encompasses at least 37 distinct structural superfamilies and more than 100 distinct structural motifs. In this paper, we examine the transcriptional regulator Wor1, a master regulator of white-opaque switching in the human fungal pathogen Candida albicans. As assessed by a variety of algorithms, this protein has no sequence or structural similarity to any known DNA-binding protein. It is, however, conserved across the vast fungal lineage, with a 300aa region of sequence conservation. Here, we show that this 300aa region of Wor1 exhibits sequence-specific DNA binding and therefore represents a new superfamily of DNA-binding proteins. We identify the 14-nucleotide-pair DNA sequence recognized by Wor1, characterize the site through mutational analysis, and demonstrate that this sequence is sufficient for the Wor1-dependent activation of transcription in vivo. Within the 300aa DNA-binding conserved region, which we have termed the WOPR box, are two domains (WOPRa and WOPRb), dissimilar to each other but especially well-conserved across the fungal lineage. We show that the WOPR box binds DNA as a monomer and that neither domain, when expressed and purified separately, exhibits sequence-specific binding. DNA binding is restored, however, when the two isolated domains are added together. These results indicate that the WOPR family of DNA-binding proteins involves an unusual coupling between two dissimilar, covalently linked domains.

Integrative genomic analyses on Ikaros and its expression related to solid cancer prognosis

Ikaros is a member of the Kruppel family of zinc finger DNA-binding proteins. The Ikaros protein contains two separate regions of zinc-finger domains: 4 DNA-binding zinc fingers near the N-terminus and 2 zinc fingers for protein-protein interactions near the C-terminus. Here, we identified the Ikaros gene from 14 vertebrate genomes and found Ikaros existed in all kinds of vertebrate including fish, amphibians, birds and mammals. Moreover, except rat and Xenopus tropicalis Ikaros proteins, which lack the first C2H2-type 1 Zinc finger region, all identified Ikaros proteins contain six C2H2-type 1 Zinc finger regions. We found human Ikaros gene showed a predominant expression in the liver, lymph node, thymus, intestine, lung, mammary gland, bone marrow, brain, heart, placenta and prostate. Moreover, four available SNPs disrupted an existing exonic splicing enhancer were identified in Ikaros. Besides the reported acute lymphoblastic leukemia (ALL), the expression of Ikaros was related to the prognosis of 13 cases of cancers including blood cancers, breast, lung, ovarian and skin cancer. Moreover, the relationship between the expression of Ikaros and prognosis varied in different cancers, even in the same cancer from different database. Two tumor-related transcriptional factor (c-Fos and Elk-1) binding sites were identified within the 1.5-kb regions upstream of the transcriptional start site of human Ikaros, which may be involved in the effect of Ikaros in tumors.

Y-box binding protein 1 is up-regulated in proliferative breast cancer and its inhibition deregulates the cell cycle

The Y-box-binding protein 1 (YB-1), a member of the cold-shock domain RNA-and DNA-binding protein family, has pleiotropic functions such as regulation of the cell cycle. The aim of this study was to evaluate if YB-1 is a proliferative marker in breast cancer and elucidate potential downstream targets involved in YB-1-mediated cell cycle regulation using RNA interference technology. YB-1 protein expression was evaluated in tissue microarrays of 131 breast invasive ductal carcinomas by immunohistochemistry, while the YB-1 gene expression profile was evaluated in the T-47D, MDA-MB-231, ZR-75-1 and MCF7 breast cancer cell lines. Silencing of the YB-1 gene in T-47D breast cancer cells was performed using siRNA and the effects of down-regulation of YB-1 on cell growth and regulation of the cell cycle were ascertained. A focused panel of 84 genes involved in cell cycle progression was also examined. In tissue microarrays, YB-1 expression was shown to be associated with proliferating cell nuclear antigen (PCNA) immunostaining. siRNA-mediated silencing of the YB-1 gene inhibited cell proliferation and induced G1 phase cell cycle arrest in T-47D breast cancer cells. Knockdown of the YB-1 gene induced up-regulation of two genes which contribute to G1-arrest (RAD9A and CDKN3 genes) and down-regulation of ten genes associated with positive regulation of the cell cycle (SKP2, SUMO1, ANAPC4, CCNB1, CKS2, MNAT1, CDC20, RBBP8, KPNA2 and CCNC genes). The data obtained from the tissue microarrays and cell lines provide evidence that YB-1 is a reliable marker of cell proliferation and possibly a potential molecular target in breast cancer therapy.

Origins of Specificity in Protein-DNA Recognition

Specific interactions between proteins and DNA are fundamental to many biological processes. In this review, we provide a revised view of protein-DNA interactions that emphasizes the importance of the three-dimensional structures of both macromolecules. We divide protein-DNA interactions into two categories: those when the protein recognizes the unique chemical signatures of the DNA bases (base readout) and those when the protein recognizes a sequence-dependent DNA shape (shape readout). We further divide base readout into those interactions that occur in the major groove from those that occur in the minor groove. Analogously, the readout of the DNA shape is subdivided into global shape recognition (for example, when the DNA helix exhibits an overall bend) and local shape recognition (for example, when a base pair step is kinked or a region of the minor groove is narrow). Based on the >1500 structures of protein-DNA complexes now available in the Protein Data Bank, we argue that individual DNA-binding proteins combine multiple readout mechanisms to achieve DNA-binding specificity. Specificity that distinguishes between families frequently involves base readout in the major groove, whereas shape readout is often exploited for higher resolution specificity, to distinguish between members within the same DNA-binding protein family.

Transcriptional regulation of cyclin-dependent kinase inhibitor 1A (P21) by the transcription factor AP-2γ

AP-2 transcription factors constitute a family of sequence-specific DNA-binding proteins encoded by five highly homologous yet functionally distinct genes, AP-2α to AP-2e. AP-2γ appears to play a major role in breast cancer, being expressed in a large proportion of primary tumours. In this study we have analysed in more detail the mechanism of transcriptional regulation of the p21/cyclin-dependent kinase inhibitor 1A (p21/CDKN1A) gene by AP-2γ.

Abstract 2248: The Y-box-binding protein 1 is associated with breast cancer progression and metastasis

Abstract The Y-box-binding protein 1 (YB-1) which belongs to the RNA- and DNA-binding protein family with a conserved cold-shock domain, is known to regulate transcription and translation. Extensive studies carried out on the multi-functional YB-1 protein have implicated its role in tumor growth and drug resistance. However, the association between YB-1 and breast cancer metastasis has not been fully investigated. To determine if YB-1 expression is correlated with breast cancer progression, we evaluated protein expression analysis in breast cancer tissue microarrays from the Singapore General Hospital by immunohistochemistry using an N-terminal YB-1 antibody and gene expression analysis in a TissueScan breast cancer tissue qPCR array (a rapid-scan cDNA panel of 48 breast cancer tissues representing breast cancer in different tumor stages) by real time RT-PCR. Next, we down-regulated the expression of the YB-1 protein in MDA-MB-231 breast cancer cells by si-RNA mediated silencing of the YB-1 gene and performed migration assays (using polycarbonate membranes of transwells separating the upper and lower chambers in 24-well plates) and invasion assays (using Matrigel-coated transwell chambers). The results show that 88.7% of breast cancer tissues were positively immunostained for the YB-1 protein and a higher YB-1 expression level was associated with axillary lymph node spread. YB-1 gene expression level in the breast cancer tissues was also higher in the advance stages of breast cancer as compared to the early stage of the tumor. In the in vitro experiments, the silencing efficiency of the YB-1 siRNA was around 90% and significant down-regulation of the YB-1 protein was verified by Western blot analysis and immunostaining of the MDA-MB-231 cells. Furthermore, siYB-1 mediated knockdown of YB-1 expression significantly reduced the migration ability and invasive potential of MDA-MB-231 cells as compared to the control group. Collectively, the data obtained from breast cancer tissues and in vitro experiments has provided evidence that YB-1 expression is associated with aggressive behavior in breast cancer. It would seem that YB-1 is a potential biomarker of metastasis in breast cancer and a promising molecular target in breast cancer therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2248.

A new member of the ribbon-helix-helix transcription factor superfamily from the plant pathogen Xanthomonas axonopodis pv. citri

XACb0070 is an uncharacterized protein coded by the two large plasmids isolated from Xanthomonas axonopodis pv. citri, the agent of citrus canker and responsible for important economical losses in citrus world production. XACb0070 presents sequence homology only with other hypothetical proteins belonging to plant pathogens, none of which have their structure determined. The NMR-derived solution structure reveals this protein is a homodimer in which each monomer presents two domains with different structural and dynamic properties: a folded N-terminal domain with beta alpha alpha topology which mediates dimerization and a long disordered C-terminal tail. The folded domain shows high structural similarity to the ribbon-helix-helix transcriptional repressors, a family of DNA-binding proteins of conserved 3D fold but low sequence homology: indeed XACb0070 binds DNA. Primary sequence and fold comparison of XACb0070 with other proteins of the ribbon-helix-helix family together with examination of the genes in the vicinity of xacb0070 suggest the protein might be the component of a toxin-antitoxin system.

The Retinal Determination Gene eyes absent Is Regulated by the EGF Receptor Pathway Throughout Development in Drosophila

Members of the Eyes absent (Eya) protein family play important roles in tissue specification and patterning by serving as both transcriptional activators and protein tyrosine phosphatases. These activities are often carried out in the context of complexes containing members of the Six and/or Dach families of DNA binding proteins. eyes absent, the founding member of the Eya family is expressed dynamically within several embryonic, larval, and adult tissues of the fruit fly, Drosophila melanogaster. Loss-of-function mutations are known to result in disruptions of the embryonic head and central nervous system as well as the adult brain and visual system, including the compound eyes. In an effort to understand how eya is regulated during development, we have carried out a genetic screen designed to identify genes that lie upstream of eya and govern its expression. We have identified a large number of putative regulators, including members of several signaling pathways. Of particular interest is the identification of both yan/anterior open and pointed, two members of the EGF Receptor (EGFR) signaling cascade. The EGFR pathway is known to regulate the activity of Eya through phosphorylation via MAPK. Our findings suggest that this pathway is also used to influence eya transcriptional levels. Together these mechanisms provide a route for greater precision in regulating a factor that is critical for the formation of a wide range of diverse tissues.