Genomes and Genes
Experts and Doctors on molecular sequence data in Huddinge, Stockholm, Sweden
Locale: Huddinge, Stockholm, Sweden
Topic: molecular sequence data
- Cerny R, Slaby I, Hammarstrom L, Wurtz T. A novel gene expressed in rat ameloblasts codes for proteins with cell binding domains. J Bone Miner Res. 1996;11:883-91 pubmed..The amelins are likely to be constituents of the enamel matrix and the only proteins that have so far been implicated in binding interactions between the ameloblast surface and its extracellular matrix...
- Shimokawa T, Rahnama F, Zaphiropoulos P. A novel first exon of the Patched1 gene is upregulated by Hedgehog signaling resulting in a protein with pathway inhibitory functions. FEBS Lett. 2004;578:157-62 pubmed..Here, we show that in both human and mouse a novel PTCH1 first exon (1C) is expressed. Exon 1C transcription is upregulated by HH signaling, but the resulting PTCH1-1C protein has a lower capacity for pathway inhibition than PTCH1-1B. ..
- Alberti S, Steffensen K, Gustafsson J. Structural characterisation of the mouse nuclear oxysterol receptor genes LXRalpha and LXRbeta. Gene. 2000;243:93-103 pubmed..Most striking is the identification of one potential NFkappaB and seven potential Ets-protein binding sites in the LXRbeta promoter, suggesting an important role for this receptor in the haematopoietic/immune system. ..
- Miranda Vizuete A, Spyrou G. Genomic structure and chromosomal localization of human thioredoxin-like protein gene (txl). DNA Seq. 2000;10:419-24 pubmed
- Zhao Y, Kacskovics I, Rabbani H, Hammarstrom L. Physical mapping of the bovine immunoglobulin heavy chain constant region gene locus. J Biol Chem. 2003;278:35024-32 pubmed..A further sequence comparison revealed that the bovine IGHC genes display an extensive polymorphism leading to expression of multiple antibody allotypes. ..
- Meining W, Eberhardt S, Bacher A, Ladenstein R. The structure of the N-terminal domain of riboflavin synthase in complex with riboflavin at 2.6A resolution. J Mol Biol. 2003;331:1053-63 pubmed..The implications for the binding specificity and the regiospecificity of the catalyzed reaction are discussed. ..
- McEwan I, Dahlman Wright K, Ford J, Wright A. Functional interaction of the c-Myc transactivation domain with the TATA binding protein: evidence for an induced fit model of transactivation domain folding. Biochemistry. 1996;35:9584-93 pubmed..These data support a model in which target factors induce or stabilize a structural conformation in activator proteins during transcriptional transactivation. ..
- Grandien K. Determination of transcription start sites in the human estrogen receptor gene and identification of a novel, tissue-specific, estrogen receptor-mRNA isoform. Mol Cell Endocrinol. 1996;116:207-12 pubmed..In addition a novel 5' untranslated exon was isolated from human liver. These results demonstrate that the human ER gene contains a third, previously not described promoter which appears to be predominantly expressed in liver. ..
- Karlstr m M, Steen I, Madern D, Fed y A, Birkeland N, Ladenstein R. The crystal structure of a hyperthermostable subfamily II isocitrate dehydrogenase from Thermotoga maritima. FEBS J. 2006;273:2851-68 pubmed publisher..The residues responsible for the binding of isocitrate and NADP+ were found to be highly conserved between TmIDH and the mammalian IDHs and it is likely that the reaction mechanism is the same...
- Liu W, Vierke G, Wenke A, Thomm M, Ladenstein R. Crystal structure of the archaeal heat shock regulator from Pyrococcus furiosus: a molecular chimera representing eukaryal and bacterial features. J Mol Biol. 2007;369:474-88 pubmed publisher..Molecular docking and mutational analyses suggested a novel binding mode in which the major specific contacts occur at the minor groove interacting with the strongly basic wing containing a cluster of three arginine residues...
- Solaroli N, Panayiotou C, Johansson M, Karlsson A. Identification of two active functional domains of human adenylate kinase 5. FEBS Lett. 2009;583:2872-6 pubmed publisher..The first domain, AK5p1, phosphorylated AMP, CMP, dAMP and dCMP with ATP or GTP as phosphate donors similarly to AK5p2. Our data demonstrate that human AK5 has two separate functional domains and that both have enzymatic activity. ..
- Antonson P, Xanthopoulos K. Molecular cloning, sequence, and expression patterns of the human gene encoding CCAAT/enhancer binding protein alpha (C/EBP alpha). Biochem Biophys Res Commun. 1995;215:106-13 pubmed..However, the expression was undetectable or very low in brain, kidney, thymus, testis and ovary. These results show that the human C/EBP alpha gene is expressed in a tissue restricted manner. ..
- Bilgin N, Lee J, Zhu H, Dalbey R, von Heijne G. Mapping of catalytically important domains in Escherichia coli leader peptidase. EMBO J. 1990;9:2717-22 pubmed
- Duan J, Nilsson L, Lambert B. Structural and functional analysis of mutations at the human hypoxanthine phosphoribosyl transferase (HPRT1) locus. Hum Mutat. 2004;23:599-611 pubmed..We have also noticed a strong correlation between mutations in the tetramer interfaces and observed phenotypes, suggesting a functional role for a tetramer transition during catalysis. ..
- Rehn A, Chalk A, Wendel M. Differential regulation of osteoadherin (OSAD) by TGF-beta1 and BMP-2. Biochem Biophys Res Commun. 2006;349:1057-64 pubmed
- Zhao Y, Pan Hammarstrom Q, Kacskovics I, Hammarstrom L. The porcine Ig delta gene: unique chimeric splicing of the first constant region domain in its heavy chain transcripts. J Immunol. 2003;171:1312-8 pubmed..However, the exon could be spliced into most of the expressed transcripts in vitro in cell transfection experiments after introduction of a single T nucleotide to restore the branchpoint sequence upstream of the putative H2 exon. ..
- Ren B, K hn J, Meslet Cladiere L, Briffotaux J, Norais C, Lavigne R, et al. Structure and function of a novel endonuclease acting on branched DNA substrates. EMBO J. 2009;28:2479-89 pubmed publisher..Altogether, our data suggest that NucS proteins constitute a new family of structure-specific DNA endonucleases that are widely distributed in archaea and in bacteria, including Mycobacterium tuberculosis...
- Burglin T. The homeobox genes of Encephalitozoon cuniculi (Microsporidia) reveal a putative mating-type locus. Dev Genes Evol. 2003;213:50-2 pubmed..Like in the mating-type locus of yeast and other fungi, one TALE and one typical homeobox are found in close proximity of each other on the chromosome, suggesting that Microsporidia also contain a mating-type locus...
- Moreno P, Geny S, Pabon Y, Bergquist H, Zaghloul E, Rocha C, et al. Development of bis-locked nucleic acid (bisLNA) oligonucleotides for efficient invasion of supercoiled duplex DNA. Nucleic Acids Res. 2013;41:3257-73 pubmed publisher..Although this first conceptual report does not address the utility of bisLNA for the targeting of DNA in a chromosomal context, it shows bisLNA as a promising candidate for interfering also with cellular genes. ..
- Nordstrand K, Sandstrom A, Aslund F, Holmgren A, Otting G, Berndt K. NMR structure of oxidized glutaredoxin 3 from Escherichia coli. J Mol Biol. 2000;303:423-32 pubmed..This could explain the observed low affinity of glutaredoxins for S-blocked glutathione analogues, in spite of the fact that glutaredoxins are highly specific reductants of glutathione mixed disulfides. ..
- Ek Rylander B, Bergman T, Andersson G. Characterization of a tartrate-resistant acid phosphatase (ATPase) from rat bone: hydrodynamic properties and N-terminal amino acid sequence. J Bone Miner Res. 1991;6:365-73 pubmed..The findings that TrATPase has a spherical shape and binds low amounts of detergent suggest that the enzyme is a soluble protein, compatible with the view that TrATPase is secreted by the osteoclast. ..
- Catchpole I, Engstrom W. Nucleotide sequence of a porcine insulin-like growth factor II cDNA. Nucleic Acids Res. 1990;18:6430 pubmed
- Wiebel F, Steffensen K, Treuter E, Feltkamp D, Gustafsson J. Ligand-independent coregulator recruitment by the triply activatable OR1/retinoid X receptor-alpha nuclear receptor heterodimer. Mol Endocrinol. 1999;13:1105-18 pubmed..Taken together, our results suggest a complex modulation of differentially induced transactivation by OR1/RXR coregulatory molecules. ..
- Visco Comandini U, Yun Z, Vahlne A, Sonnerborg A. No association of HIV type 1 long terminal repeat sequence pattern with long-term nonprogression and in vivo viral replication levels in European subjects. AIDS Res Hum Retroviruses. 1999;15:609-17 pubmed..Our results suggest that HIV-1 LTR defects are rare among Italian and Swedish LTNPs. ..
- Zaphiropoulos P, Unden A, Rahnama F, Hollingsworth R, Toftgard R. PTCH2, a novel human patched gene, undergoing alternative splicing and up-regulated in basal cell carcinomas. Cancer Res. 1999;59:787-92 pubmed..This finding tightly links PTCH2 with the sonic hedgehog/PTCH signaling pathway, implying that PTCH2 has related, but yet distinct, functions than PTCH1. ..
- Baumann H, Paulsen K, Kovacs H, Berglund H, Wright A, Gustafsson J, et al. Refined solution structure of the glucocorticoid receptor DNA-binding domain. Biochemistry. 1993;32:13463-71 pubmed..8 A. The most pronounced differences between the free and DNA-complexed states are found within the fragment C476-C482 in the second zinc-coordinating domain.(ABSTRACT TRUNCATED AT 250 WORDS) ..
- Agback P, Baumann H, Knapp S, Ladenstein R, Hard T. Architecture of nonspecific protein-DNA interactions in the Sso7d-DNA complex. Nat Struct Biol. 1998;5:579-84 pubmed..Sso7d binding also distorts the DNA conformation and introduces significant unwinding of the helix. This effect suggests a mechanism for DNA packing in Sulfolobus based on negative DNA supercoiling. ..
- Baumann H, Knapp S, Karshikoff A, Ladenstein R, Hard T. DNA-binding surface of the Sso7d protein from Sulfolobus solfataricus. J Mol Biol. 1995;247:840-6 pubmed..We note that the five (of 14) lysine side-chains that are specifically subjected to N zeta-monomethylation in the cell are located on surfaces of Sso7d that are exposed to the solvent in the proposed Sso7d-DNA complex. ..
- Guardiola Diaz H, Rehnmark S, Usuda N, Albrektsen T, Feltkamp D, Gustafsson J, et al. Rat peroxisome proliferator-activated receptors and brown adipose tissue function during cold acclimatization. J Biol Chem. 1999;274:23368-77 pubmed
- Shimokawa T, Tostar U, Lauth M, Palaniswamy R, Kasper M, Toftgard R, et al. Novel human glioma-associated oncogene 1 (GLI1) splice variants reveal distinct mechanisms in the terminal transduction of the hedgehog signal. J Biol Chem. 2008;283:14345-54 pubmed publisher..Collectively, our findings reveal that the activation mechanism of the terminal transducer of the pathway, GLI1, is mediated not only by GLI1FL but also by the GLI1DeltaN variant. ..
- Vihinen M, Zvelebil M, Zhu Q, Brooimans R, Ochs H, Zegers B, et al. Structural basis for pleckstrin homology domain mutations in X-linked agammaglobulinemia. Biochemistry. 1995;34:1475-81 pubmed..The mutated residues F25, V64, and V113, and possibly residue(s) around Q103, could form a binding site, since these amino acids are located close to each other on the surface of the molecule. ..
- Vihinen M, Vetrie D, Maniar H, Ochs H, Zhu Q, Vorechovsky I, et al. Structural basis for chromosome X-linked agammaglobulinemia: a tyrosine kinase disease. Proc Natl Acad Sci U S A. 1994;91:12803-7 pubmed
- Smith C, Baskin B, Humire Greiff P, Zhou J, Olsson P, Maniar H, et al. Expression of Bruton's agammaglobulinemia tyrosine kinase gene, BTK, is selectively down-regulated in T lymphocytes and plasma cells. J Immunol. 1994;152:557-65 pubmed..Our findings are compatible with a general expression of the BTK gene in hematopoietic cells, except in T lymphocytes and plasma cells, in which the transcript level is selectively down-regulated. ..
- Gearing K, Gottlicher M, Teboul M, Widmark E, Gustafsson J. Interaction of the peroxisome-proliferator-activated receptor and retinoid X receptor. Proc Natl Acad Sci U S A. 1993;90:1440-4 pubmed..These results raise the possibility of convergence of the PPAR and retinoid-dependent signaling pathways on promoters containing PPRE-like responsive elements. ..
- Ohyama Y, Meaney S, Heverin M, Ekström L, Brafman A, Shafir M, et al. Studies on the transcriptional regulation of cholesterol 24-hydroxylase (CYP46A1): marked insensitivity toward different regulatory axes. J Biol Chem. 2006;281:3810-20 pubmed..The failure to demonstrate a significant transcriptional regulation under most conditions is discussed in relation to the turnover of brain and neuronal cholesterol. ..
- Hard T, Barnes H, Larsson C, Gustafsson J, Lund J. Solution structure of a mammalian PCB-binding protein in complex with a PCB. Nat Struct Biol. 1995;2:983-9 pubmed..Breakage of these bonds induces a local unfolding of the N- and C-termini and a separation of helices creating a channel into the binding site. These effects make the ligand binding cavity readily accessible to entry of the ligand. ..
- Rowlands J, McEwan I, Gustafsson J. Trans-activation by the human aryl hydrocarbon receptor and aryl hydrocarbon receptor nuclear translocator proteins: direct interactions with basal transcription factors. Mol Pharmacol. 1996;50:538-48 pubmed..Taken together, these results suggest that AhR and ARNT activate target gene expression, at least in part, through direct interactions with basal transcription factors. ..
- Eggertsen G, Olin M, Andersson U, Ishida H, Kubota S, Hellman U, et al. Molecular cloning and expression of rabbit sterol 12alpha-hydroxylase. J Biol Chem. 1996;271:32269-75 pubmed..5 and 4.5 kilobases, respectively. Fasting of rats and mice led to a severalfold increase in both enzyme activity and mRNA levels. In contrast, starvation of rabbits had little or no stimulatory effect on enzyme activity and mRNA levels. ..
- Steglich B, Filion G, van Steensel B, Ekwall K. The inner nuclear membrane proteins Man1 and Ima1 link to two different types of chromatin at the nuclear periphery in S. pombe. Nucleus. 2012;3:77-87 pubmed..Our results point to a role of nuclear membrane proteins in organizing chromatin domains and loops. ..
- Treuter E, Albrektsen T, Johansson L, Leers J, Gustafsson J. A regulatory role for RIP140 in nuclear receptor activation. Mol Endocrinol. 1998;12:864-81 pubmed
- Duan J, Dahlback B, Villoutreix B. Proposed lipocalin fold for apolipoprotein M based on bioinformatics and site-directed mutagenesis. FEBS Lett. 2001;499:127-32 pubmed..ApoM displays two strong acidic patches of potential functional importance, one around the N-terminus and the other next to the opening of the beta-barrel. ..
- Sommer W, Arlinde C, Caberlotto L, Thorsell A, Hyytia P, Heilig M. Differential expression of diacylglycerol kinase iota and L18A mRNAs in the brains of alcohol-preferring AA and alcohol-avoiding ANA rats. Mol Psychiatry. 2001;6:103-8; 5 pubmed..Differential display RT-PCR seems to provide a feasible strategy to identify previously unknown genes whose differential expression correlates with behavioral phenotypes related to dependence. ..
- Zhang X, Meining W, Fischer M, Bacher A, Ladenstein R. X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 A resolution: determinants of thermostability revealed from structural comparisons. J Mol Biol. 2001;306:1099-114 pubmed..The findings indicate the influence of the optimization of hydrophobic and ionic contacts in gaining thermostability. ..
- Finta C, Zaphiropoulos P. The human cytochrome P450 3A locus. Gene evolution by capture of downstream exons. Gene. 2000;260:13-23 pubmed..These findings may represent a generalized evolutionary process with genes having the potential to capture neighboring sequences and use them as functional exons. ..
- Gustafsson M, Hussain A, Mohammad D, Mohamed A, Nguyen V, Metalnikov P, et al. Regulation of nucleocytoplasmic shuttling of Bruton's tyrosine kinase (Btk) through a novel SH3-dependent interaction with ankyrin repeat domain 54 (ANKRD54). Mol Cell Biol. 2012;32:2440-53 pubmed publisher..Liar is the first protein identified that specifically influences the nucleocytoplasmic shuttling of Btk and Txk and belongs to a rare group of known proteins carrying out this activity in a Crm1-dependent manner. ..
- Bjerling P, Ekwall K, Egel R, Thon G. A novel type of silencing factor, Clr2, is necessary for transcriptional silencing at various chromosomal locations in the fission yeast Schizosaccharomyces pombe. Nucleic Acids Res. 2004;32:4421-8 pubmed..Using chromatin immunoprecipitation, we show that Clr2 is necessary for histone hypoacetylation in the mating-type region, suggesting that Clr2 acts upstream of histone deacetylases to promote transcriptional silencing. ..
- Tapia Paez I, Tammimies K, Massinen S, Roy A, Kere J. The complex of TFII-I, PARP1, and SFPQ proteins regulates the DYX1C1 gene implicated in neuronal migration and dyslexia. FASEB J. 2008;22:3001-9 pubmed publisher..Furthermore, allelic differences in the promoter or 5' untranslated region of DYX1C1 may affect factor binding and thus regulation of the gene. ..
- Kitambi S, Hauptmann G. The zebrafish orphan nuclear receptor genes nr2e1 and nr2e3 are expressed in developing eye and forebrain. Gene Expr Patterns. 2007;7:521-8 pubmed..In both structures, nr2e3 expression was found in photoreceptor cells. The developmental expression profile of zebrafish nr2e1 and nr2e3 is consistent with evolutionary conserved functions in eye and rostral brain structures. ..
- McGuire J, Coumailleau P, Whitelaw M, Gustafsson J, Poellinger L. The basic helix-loop-helix/PAS factor Sim is associated with hsp90. Implications for regulation by interaction with partner factors. J Biol Chem. 1995;270:31353-7 pubmed..These results indicate that hsp90 may play a role in conditional regulation of Sim function, and that Per and possibly bHLH/PAS partner factors may activate Sim by inducing release of hsp90 during the dimerization process. ..
- Antonson P, Stellan B, Yamanaka R, Xanthopoulos K. A novel human CCAAT/enhancer binding protein gene, C/EBPepsilon, is expressed in cells of lymphoid and myeloid lineages and is localized on chromosome 14q11.2 close to the T-cell receptor alpha/delta locus. Genomics. 1996;35:30-8 pubmed
- Zaphiropoulos P, Toftgard R. cDNA cloning of a novel WD repeat protein mapping to the 9q22.3 chromosomal region. DNA Cell Biol. 1996;15:1049-56 pubmed..Finally, Southern analysis showed a functional conservation of the WD repeat protein in various species. ..
- Allard P, Rak A, Wimberly B, Clemons W, Kalinin A, Helgstrand M, et al. Another piece of the ribosome: solution structure of S16 and its location in the 30S subunit. Structure. 2000;8:875-82 pubmed..Overall, this work exemplifies the benefits of combining high-resolution nuclear magnetic resonance (NMR) structures of individual components with low-resolution X-ray maps to elucidate structures of large complexes. ..
- Miranda Vizuete A, Damdimopoulos A, Spyrou G. cDNA cloning, expression and chromosomal localization of the mouse mitochondrial thioredoxin reductase gene(1). Biochim Biophys Acta. 1999;1447:113-8 pubmed..Finally, we have assigned the mouse TrxR2 gene to chromosome 16 mapping at 11.2 cM from the centromer and linked to the catechol-o-methyltransferase (comt) gene. ..