当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Hormonal regulation of the E75 gene in Drosophila: identifying functional regulatory elements through computational and biological analysis.

Hormonal regulation of the E75 gene in Drosophila: identifying functional regulatory elements through computational and biological analysis.

Abstract：

:Drosophila development is regulated by two hormones, 20-hydroxyecdysone (ecdysone) and juvenile hormone. We previously found that expression of the E75 gene is induced by both hormones in cultured S2 cells. E75 occupies over 100 kb of genomic DNA; it has four alternative promoters producing isoforms E75A, E75B, E75C, and E75D. To identify hormone response elements in the 60-kb noncoding area upstream of the E75A transcription start site, we developed a novel approach combining in vitro, in vivo, and in silico techniques. Using chromatin immunoprecipitation coupled with quantitative real-time PCR, we identified five putative enhancers marked with H3K4 monomethylation and depletion of H3. Four of these are ecdysone-regulated enhancers, which possess hormone-responsive chromatin and contain sequences sufficient to confer ecdysone inducibility to a reporter gene. Using EvoPrinterHD- and Multiple Expectation Maximization for Motif Elicitation-based computational analysis, we first created a database of short sequences that are highly conserved among 12 Drosophila species. Within this database, we then identified a set of putative ecdysone response elements (EcREs). Seven of these elements represent in vivo binding sites for the ecdysone receptor and are necessary for hormone-mediated activation of gene expression in cultured cells. We found that each EcRE exhibits different binding and activation properties, and at least some of them function cooperatively.We propose that the presence of multiple EcREs with distinct features provides flexibility to the rapid and powerful response of E75A to ecdysone during Drosophila development.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Bernardo TJ,Dubrovskaya VA,Jannat H,Maughan B,Dubrovsky EB

doi

10.1016/j.jmb.2009.02.013

subject

Has Abstract

pub_date

2009-04-10 00:00:00

pages

794-808

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(09)00152-1

journal_volume

387

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Guided evolution of enzymes with new substrate specificities.

    abstract：:A gene library was constructed coding for all possible variants of two amino acids (101, 102) in a solvent-exposed surface return loop (alpha E-beta D) of Bacillus stearothermophilus L-lactate dehydrogenase (bsLDH). All but one of 38 enzyme variants examined were thermally stable and had native-like hydrodynamic prope...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0626

    authors： el Hawrani AS,Sessions RB,Moreton KM,Holbrook JJ

    更新日期：1996-11-22 00:00:00

  • X-ray structure of the quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa: basis of substrate specificity.

    abstract：:The homodimeric enzyme form of quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa ATCC 17933 crystallizes readily with the space group R3. The X-ray structure was solved at 2.6 A resolution by molecular replacement. Aside from differences in some loops, the folding of the enzyme is very similar to the larg...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3603

    authors： Keitel T,Diehl A,Knaute T,Stezowski JJ,Höhne W,Görisch H

    更新日期：2000-04-07 00:00:00

  • Characterization of the interaction of GABARAPL-1 with the LIR motif of NBR1.

    abstract：:Selective autophagy requires the specific segregation of targeted proteins into autophagosomes. The selectivity is mediated by autophagy receptors, such as p62 and NBR1, which can bind to autophagic effector proteins (Atg8 in yeast, MAP1LC3 protein family in mammals) anchored in the membrane of autophagosomes. Recogni...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.05.003

    authors： Rozenknop A,Rogov VV,Rogova NY,Löhr F,Güntert P,Dikic I,Dötsch V

    更新日期：2011-07-15 00:00:00

  • High-resolution structure of ybfF from Escherichia coli K12: a unique substrate-binding crevice generated by domain arrangement.

    abstract：:Esterases are one of the most common enzymes and are involved in diverse cellular functions. ybfF protein from Escherichia coli (Ec_ybfF) belongs to the esterase family for the large substrates, palmitoyl coenzyme A and malonyl coenzyme A, which are important cellular intermediates for energy conversion and biomolecul...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.12.062

    authors： Park SY,Lee SH,Lee J,Nishi K,Kim YS,Jung CH,Kim JS

    更新日期：2008-03-07 00:00:00

  • The replisome organizer (G38P) of Bacillus subtilis bacteriophage SPP1 forms specialized nucleoprotein complexes with two discrete distant regions of the SPP1 genome.

    abstract：:Initiation of Bacillus subtilis bacteriophage SPP1 DNA replication requires the products of genes 38, 39 and 40 (G38P, G39P and G40P). G38P specifically binds two discrete regions, which are 32.1 kb apart in a linear map of the SPP1 genome. One of these target sites, which maps at the left end of the phage genome, wit...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1060

    authors： Missich R,Weise F,Chai S,Lurz R,Pedré X,Alonso JC

    更新日期：1997-07-04 00:00:00

  • Analysis of protein main-chain solvation as a function of secondary structure.

    abstract：:We have analysed the hydration of main-chain carbonyl and amide groups in 24 high-resolution well-refined protein structures as a function of the secondary structure in which these polar groups occur. We find that main-chain atoms in beta-sheets are as hydrated as those in alpha-helices, with most interactions involvi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)80080-e

    authors： Thanki N,Umrania Y,Thornton JM,Goodfellow JM

    更新日期：1991-09-20 00:00:00

  • Molecular structure of fd (f1, M13) filamentous bacteriophage refined with respect to X-ray fibre diffraction and solid-state NMR data supports specific models of phage assembly at the bacterial membrane.

    abstract：:Filamentous bacteriophage (Inovirus) is a simple and well-characterized model system. The phage particle, or virion, is about 60 angstroms in diameter and several thousand angstrom units long. The virions are assembled at the bacterial membrane as they extrude out of the host without killing it, an example of specific...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.10.048

    authors： Marvin DA,Welsh LC,Symmons MF,Scott WR,Straus SK

    更新日期：2006-01-13 00:00:00

  • Two-dimensional kinetics of inter-connexin interactions from single-molecule force spectroscopy.

    abstract：:Gap junction channels are intercellular channels that form by docking the extracellular loops of connexin protein subunits. While the structure and function of gap junctions as intercellular channels have been characterized using different techniques, the physics of the inter-connexin interaction remain unknown. Moreo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.07.013

    authors： Rico F,Oshima A,Hinterdorfer P,Fujiyoshi Y,Scheuring S

    更新日期：2011-09-09 00:00:00

  • Heterocyst-forming filamentous cyanobacteria encode proteins that resemble eukaryotic RNA-binding proteins of the RNP family.

    abstract：:Heterocyst-forming cyanobacteria have multiple genes encoding proteins that are similar to the RNP family of eukaryotic RNA-binding proteins. Three genes from two strains of cyanobacteria (Anabaena and Chlorogloeopsis) have been sequenced. All three putative gene products contain a single RNA Recognition Motif (RRM) t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1070

    authors： Mulligan ME,Jackman DM,Murphy ST

    更新日期：1994-01-21 00:00:00

  • Rz/Rz1 lysis gene equivalents in phages of Gram-negative hosts.

    abstract：:Under usual laboratory conditions, lysis by bacteriophage lambda requires only the holin and endolysin genes, but not the Rz and Rz1 genes, of the lysis cassette. Defects in Rz or Rz1 block lysis only in the presence of high concentrations of divalent cations. The lambda Rz and Rz1 lysis genes are remarkable in that R...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.08.045

    authors： Summer EJ,Berry J,Tran TA,Niu L,Struck DK,Young R

    更新日期：2007-11-09 00:00:00

  • Isoform-Specific Phosphorylation in Human Hsp90β Affects Interaction with Clients and the Cochaperone Cdc37.

    abstract：:The 90-kDa heat shock proteins (Hsp90s) assist the maturation of many key regulators of signal transduction pathways and cellular control circuits like protein kinases and transcription factors and chaperone their stability and activity. In this function, Hsp90s cooperate with some 30 cochaperones and they are themsel...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2017.01.011

    authors： Nguyen MTN,Knieß RA,Daturpalli S,Le Breton L,Ke X,Chen X,Mayer MP

    更新日期：2017-03-10 00:00:00

  • Single molecule force spectroscopy of spectrin repeats: low unfolding forces in helix bundles.

    abstract：:Spectrin repeats fold into triple helical coiled-coils comprising approximately 106 amino acid residues. Using an AFM-related technique we measured the force required to mechanically unfold these repeats to be 25 to 35 pN. Under tension, individual spectrin repeats unfold independently and in an all-or-none process. T...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2466

    authors： Rief M,Pascual J,Saraste M,Gaub HE

    更新日期：1999-02-19 00:00:00

  • Premature stop codons inactivate the RT6 genes of the human and chimpanzee species.

    abstract：:RT6 is a glycosyl phosphatidylinositol-anchored cell membrane protein, whose expression is restricted to peripheral T cells and intraepithelial lymphocytes. It has attracted interest as a T cell differentiation marker and activation antigen in rats. The only known protein to which RT6 shows significant homology is a r...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1680

    authors： Haag F,Koch-Nolte F,Kühl M,Lorenzen S,Thiele HG

    更新日期：1994-10-28 00:00:00

  • Atomic environment energies in proteins defined from statistics of accessible and contact surface areas.

    abstract：:Atomic contact potentials are derived by statistical analysis of atomic surface contact areas versus atom type in a database of non-homologous protein structures. The atomic environment is characterized by the surface area accessible to solvent and the surface of contacts with polar and non-polar atoms. Four types of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1006/jmbi.1995.0328

    authors： Delarue M,Koehl P

    更新日期：1995-06-09 00:00:00

  • NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove.

    abstract：:The integrase protein (Int) from bacteriophage lambda is the archetypal member of the tyrosine recombinase family, a large group of enzymes that rearrange DNA in all domains of life. Int catalyzes the insertion and excision of the viral genome into and out of the Escherichia coli chromosome. Recombination transpires w...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.03.041

    authors： Fadeev EA,Sam MD,Clubb RT

    更新日期：2009-05-15 00:00:00

  • Preliminary crystallographic study of glycosylated recombinant human renin.

    abstract：:Single crystals of glycosylated recombinant human renin have been obtained using the hanging-drop vapor diffusion method with polyethylene glycol and sodium chloride as coprecipitants. The crystals belong to the cubic space group P2(1)3 with a = 143.0 A and contain two molecules of renin in the asymmetric unit. A self...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90305-7

    authors： Lim LW,Stegeman RA,Leimgruber NK,Gierse JK,Abdel-Meguid SS

    更新日期：1989-11-05 00:00:00

  • Structural and thermodynamic insights into the recognition of native proteins by anti-peptide antibodies.

    abstract：:The mechanism by which antibodies elicited against protein-derived peptides achieve cross-reactivity with their cognate proteins remains unknown. To address this question, we have carried out the complete thermodynamic characterization of the association of a monoclonal antibody (260.33.12) raised against a peptide (S...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2013.02.031

    authors： Armstrong A,Hildreth JEK,Amzel LM

    更新日期：2013-06-12 00:00:00

  • Changes in side-chain and backbone dynamics identify determinants of specificity in RNA recognition by human U1A protein.

    abstract：:The ribonucleoprotein (RNP) domain is one of the most common eukaryotic protein domains, and is found in many proteins involved in recognition of a wide variety of RNAs. Two structures of RNA complexes of human U1A protein have revealed important aspects of RNP-RNA recognition, but have also raised intriguing question...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3311

    authors： Mittermaier A,Varani L,Muhandiram DR,Kay LE,Varani G

    更新日期：1999-12-10 00:00:00

  • Dissection of the promoter region of the inositol 1,4,5-trisphosphate receptor gene, itr-1, in C. elegans: a molecular basis for cell-specific expression of IP3R isoforms.

    abstract：:Inositol 1,4,5-trisphosphate receptors in Caenorhabditis elegans are encoded by a single gene, itr-1. This provides a powerful system in which to dissect the mechanisms that control the tissue-specific expression of molecules that determine the specificity of calcium signalling. We first identified the Caenorhabditis ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4388

    authors： Gower NJ,Temple GR,Schein JE,Marra M,Walker DS,Baylis HA

    更新日期：2001-02-16 00:00:00

  • Common physical properties of DNA affecting target site selection of sleeping beauty and other Tc1/mariner transposable elements.

    abstract：:Sleeping Beauty (SB) is the most active Tc1/mariner-type transposable element in vertebrates, and is therefore a valuable vector for transposon mutagenesis in vertebrate models and for human gene therapy. We have analyzed factors affecting target site selection of SB in mammalian cells, by generating transposition eve...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)00991-9

    authors： Vigdal TJ,Kaufman CD,Izsvák Z,Voytas DF,Ivics Z

    更新日期：2002-10-25 00:00:00

  • Infrared dichroism of twisted beta-sheet barrels. The structure of E. coli outer membrane proteins.

    abstract：:The infrared dichroic ratios of the amide bands from oriented beta-barrels yield an experimental value for the mean orientation, beta, of the beta-strands, relative to the barrel axis. For a barrel of n strands, this then gives the shear number, S, that characterizes the stagger of the beta-sheet. Combining values of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3557

    authors： Marsh D

    更新日期：2000-03-31 00:00:00

  • Beta2-microglobulin amyloidosis: insights from conservation analysis and fibril modelling by protein docking techniques.

    abstract：:Current data suggest that globular domains may form amyloids via different mechanisms. Nevertheless, there are indications that the initiation of the process takes place invariably in the less stable segments of a protein domain. We have studied the sequence and structural conservation of beta(2)-microglobulin that de...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00557-6

    authors： Benyamini H,Gunasekaran K,Wolfson H,Nussinov R

    更新日期：2003-06-27 00:00:00

  • Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme.

    abstract：:Although largely deemed as structurally conserved, catalytic metal ion sites can rearrange, thereby contributing to enzyme evolvability. Here, we show that in paraoxonase-1, a lipo-lactonase, catalytic promiscuity and divergence into an organophosphate hydrolase are correlated with an alternative mode of the catalytic...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2013.01.009

    authors： Ben-David M,Wieczorek G,Elias M,Silman I,Sussman JL,Tawfik DS

    更新日期：2013-03-25 00:00:00

  • Transcription from the rha operon psr promoter.

    abstract：:S1 nuclease mapping experiments performed with RNA extracted from cell lines that were unable to metabolize L-rhamnose demonstrated that L-rhamnose and not a metabolite was the inducer of the L-rhamnose operons of Escherichia coli. In vitro transcription studies showed that purified RhaR activates transcription from t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(90)90003-5

    authors： Tobin JF,Schleif RF

    更新日期：1990-01-05 00:00:00

  • Interdomain contact regions and angles between adjacent short consensus repeat domains.

    abstract：:The short consensus repeat domain (SCR, complement control protein module, sushi-domain) is a structural unit found in multiple adjacent copies in more than 40 human proteins. Each bead-like domain is composed of approximately 60 residues and the adjacent domains are connected in a head-to-tail fashion with linkers th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.10.017

    authors： Lehtinen MJ,Meri S,Jokiranta TS

    更新日期：2004-12-10 00:00:00

  • The immunoglobulin-like domains 1 and 2 of the protein tyrosine phosphatase LAR adopt an unusual horseshoe-like conformation.

    abstract：:Neurogenesis depends on exquisitely regulated interactions between macromolecules on the cell surface and in the extracellular matrix. In particular, interactions between proteoglycans and members of the type IIa subgroup of receptor protein tyrosine phosphatases underlie crucial developmental processes such as the fo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.03.013

    authors： Biersmith BH,Hammel M,Geisbrecht ER,Bouyain S

    更新日期：2011-05-13 00:00:00

  • MPTherm-Pred: Analysis and Prediction of Thermal Stability Changes upon Mutations in Transmembrane Proteins.

    abstract：:The stability of membrane proteins differs from globular proteins due to the presence of nonpolar membrane-spanning regions. Using a dataset of 929 membrane protein mutations whose effects on thermal stability (ΔTm) were experimentally determined, we found that the average ΔTm due to 190 stabilizing and 232 destabiliz...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2020.09.005

    authors： Kulandaisamy A,Zaucha J,Frishman D,Gromiha MM

    更新日期：2020-09-10 00:00:00

  • Translational control and differential RNA decay are key elements regulating postsegregational expression of the killer protein encoded by the parB locus of plasmid R1.

    abstract：:The parB locus of plasmid R1, which mediates plasmid stability via postsegregational killing of plasmid-free cells, encodes two genes, hok and sok. The hok gene product is a potent cell-killing protein. The hok gene is regulated at the translational level by the sok gene-encoded repressor, a small anti-sense RNA compl...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90096-4

    authors： Gerdes K,Helin K,Christensen OW,Løbner-Olesen A

    更新日期：1988-09-05 00:00:00

  • Architecture of the Complex Formed by Large and Small Terminase Subunits from Bacteriophage P22.

    abstract：:Packaging of viral genomes inside empty procapsids is driven by a powerful ATP-hydrolyzing motor, formed in many double-stranded DNA viruses by a complex of a small terminase (S-terminase) subunit and a large terminase (L-terminase) subunit, transiently docked at the portal vertex during genome packaging. Despite rece...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2015.08.013

    authors： McNulty R,Lokareddy RK,Roy A,Yang Y,Lander GC,Heck AJR,Johnson JE,Cingolani G

    更新日期：2015-10-09 00:00:00

  • Structural insight into how an anti-idiotypic antibody against D3H44 (anti-tissue factor antibody) restores normal coagulation.

    abstract：:6A6 is a murine monoclonal antibody raised against the humanized anti-tissue factor antibody D3H44. 6A6 is able to completely neutralize the anticoagulant activity of D3H44 in tissue factor-dependent functional assays, such as endotoxin-induced whole blood clotting, prothrombin time, as well as factor X and factor IX ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00735-6

    authors： Eigenbrot C,Meng YG,Krishnamurthy R,Lipari MT,Presta L,Devaux B,Wong T,Moran P,Bullens S,Kirchhofer D

    更新日期：2003-08-08 00:00:00