103 results on '"Aasland, R"'
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2. Multi-author Review¶Epigenetic control of transcription¶Introduction: the genetics of epigenetics
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Gasser, S. M., Paro, R., Stewart, F., and Aasland, R.
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- 1998
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3. Proteins Associated with Chromatin from Escherichia coli
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Lossius, I., Holck, A., Aasland, R., Haarr, L., Kleppe, K., Gualerzi, Claudio O., editor, and Pon, Cynthia L., editor
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- 1986
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4. The ELM server: A new source for revealing short functional sites in modular eukaryotic proteins. Nucleic Acids Res., 31(13):3625-30
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Puntervoll, P, Linding, R, Gemnd, C, CHABANIS DAVIDSON, S, Ramu, C, Mattingsdal, M, Cameron, S, Martin, D. M. A., Ausiello, G, Brannetti, B, Costantini, A, Ferr, F, Maselli, V, Via, Allegra, Cesareni, G, Diella, F, SUPERTI FURGA, G, Wyrwicz, L, Mcguigan, C, Gudavalli, R, Letunic, I, Bork, P, Rychlewski, L, Kster, B, HELMER CITTERICH, M, Hunter, W. N., Aasland, R., and Gibson, T. J.
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- 2003
5. Structure of an active form of mammalian AMPK
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Xiao, B., primary, Sanders, M.J., additional, Underwood, E., additional, Heath, R., additional, Mayer, F., additional, Carmena, D., additional, Jing, C., additional, Walker, P.A., additional, Eccleston, J.F., additional, Haire, L.F., additional, Saiu, P., additional, Howell, S.A., additional, Aasland, R., additional, Martin, S.R., additional, Carling, D., additional, and Gamblin, S.J., additional
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- 2013
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6. ASHH2 a CW domain
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Kristiansen, P., primary, Hoppmann, V., additional, Thorstensen, T., additional, Aalen, R.B., additional, Aasland, R., additional, Finne, K., additional, and Veiseth, S., additional
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- 2011
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7. Structure of the regulatory fragment of mammalian AMPK in complex with one ADP
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Xiao, B., primary, Sanders, M.J., additional, Underwood, E., additional, Heath, R., additional, Mayer, F., additional, Carmena, D., additional, Jing, C., additional, Walker, P.A., additional, Eccleston, J.F., additional, Haire, L.F., additional, Saiu, P., additional, Howell, S.A., additional, Aasland, R., additional, Martin, S.R., additional, Carling, D., additional, and Gamblin, S.J., additional
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- 2011
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8. Structure of an active form of mammalian AMPK
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Xiao, B., primary, Sanders, M.J., additional, Underwood, E., additional, Heath, R., additional, Mayer, F., additional, Carmena, D., additional, Jing, C., additional, Walker, P.A., additional, Eccleston, J.F., additional, Haire, L.F., additional, Saiu, P., additional, Howell, S.A., additional, Aasland, R., additional, Martin, S.R., additional, Carling, D., additional, and Gamblin, S.J., additional
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- 2011
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9. Structure of the regulatory fragment of mammalian aMPK in complex with two ADP
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Xiao, B., primary, Sanders, M.J., additional, Underwood, E., additional, Heath, R., additional, Mayer, F., additional, Carmena, D., additional, Jing, C., additional, Walker, P.A., additional, Eccleston, J.F., additional, Haire, L.F., additional, Saiu, P., additional, Howell, S.A., additional, Aasland, R., additional, Martin, S.R., additional, Carling, D., additional, and Gamblin, S.J., additional
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- 2011
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10. STRUCTURE OF THE REGULATORY FRAGMENT OF MAMMALIAN AMPK IN COMPLEX WITH COUMARIN ADP
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Xiao, B., primary, Sanders, M.J., additional, Underwood, E., additional, Heath, R., additional, Mayer, F., additional, Carmena, D., additional, Jing, C., additional, Walker, P.A., additional, Eccleston, J.F., additional, Haire, L.F., additional, Saiu, P., additional, Howell, S.A., additional, Aasland, R., additional, Martin, S.R., additional, Carling, D., additional, and Gamblin, S.J., additional
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- 2011
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11. Cell biologyPaper alert
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DESAI, A, primary, HOLLERAN, E, additional, ROCHE, S, additional, AASLAND, R, additional, WEINZIERL, R, additional, IZAURRALDE, E, additional, MATTER, K, additional, SLESINGER, P, additional, PFAFF, M, additional, and HUCKRIEDE, N, additional
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- 1999
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12. FYVE-finger proteins--effectors of an inositol lipid
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Stenmark, H., primary and Aasland, R., additional
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- 1999
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13. Two variants of the pituitary specific transcription factor Pit-1 in Atlantic salmon
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Lorens, J B, primary, Aasland, R, additional, Brunstad, H, additional, Bergh, H, additional, and Male, R, additional
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- 1996
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14. The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB
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Aasland, R, primary
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- 1996
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15. The PHD finger: Implications for chromatin-mediated transcriptional regulation
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Aasland, R, primary
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- 1995
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16. Expression of growth hormone genes in Atlantic salmon
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Lorens, J B, primary, Nerland, A H, additional, Aasland, R, additional, Lossius, I, additional, and Male, R, additional
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- 1993
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17. Co‐expression of the genes encoding transforming growth factor‐α and its receptor in papillary carcinomas of the thyroid
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Aasland, R., primary, Akslen, L. A., additional, Varhaug, J. E., additional, and Lillehaug, J. R., additional
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- 1990
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18. Introduction: the genetics of epigenetics
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Gasser, S. M., Paro, R., Stewart, F., and Aasland, R.
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- 1998
19. Expression of oncogenes in thyroid tumours: coexpression of c-erbB2/neu and c-erbB.
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Aasland, R, Lillehaug, JR, Male, R, Jøsendal, O, Varhaug, JE, and Kleppe, K
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- 1988
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20. The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program.
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Pijnappel, W W, Schaft, D, Roguev, A, Shevchenko, A, Tekotte, H, Wilm, M, Rigaut, G, Séraphin, B, Aasland, R, and Stewart, A F
- Abstract
Set3 is one of two proteins in the yeast Saccharomyces cerevisiae that, like Drosophila Trithorax, contains both SET and PHD domains. We found that Set3 forms a single complex, Set3C, with Snt1, YIL112w, Sif2, Cpr1, and two putative histone deacetylases, Hos2 and NAD-dependent Hst1. Set3C includes NAD-dependent and independent deacetylase activities when assayed in vitro. Homology searches suggest that Set3C is the yeast analog of the mammalian HDAC3/SMRT complex. Set3C represses genes in early/middle of the yeast sporulation program, including the key meiotic regulators ime2 and ndt80. Whereas Hos2 is only found in Set3C, Hst1 is also present in a complex with Sum1, supporting previous characterizations of Hst1 and Sum1 as repressors of middle sporulation genes during vegetative growth. However, Hst1 is not required for meiotic repression by Set3C, thus implying that Set3C (-Hst1) and not Hst1-Sum1, is the meiotic-specific repressor of early/middle sporulation genes.
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- 2001
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21. Molecular cloning of human uracil‐DNA glycosylase, a highly conserved DNA repair enzyme.
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Olsen, L.C., Aasland, R., Wittwer, C.U., Krokan, H.E., and Helland, D.E.
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Uracil‐DNA glycosylase is the DNA repair enzyme responsible for the removal of uracil from DNA, and it is present in all organisms investigated. Here we report on the cloning and sequencing of a cDNA encoding the human uracil‐DNA glycosylase. The sequences of uracil‐DNA glycosylases from yeast, Escherichia coli, herpes simplex virus type 1 and 2, and homologous genes from varicella‐zoster and Epstein‐Barr viruses are known. It is shown in this report that the predicted amino acid sequence of the human uracil‐DNA glycosylase shows a striking similarity to the other uracil‐DNA glycosylases, ranging from 40.3 to 55.7% identical residues. The proteins of human and bacterial origin were unexpectedly found to be most closely related, 73.3% similarity when conservative amino acid substitutions were included. The similarity between the different uracil‐DNA glycosylase genes is confined to several discrete boxes. These findings strongly indicate that uracil‐DNA glycosylases from phylogenetically distant species are highly conserved.
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- 1989
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22. A vase-like gene in zebrafish identifies putative primordial germ cells
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Olsen, L. C., Aasland, R., and Fjose, A.
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- 1997
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23. Purification and characterization of the 17 K protein, a DNA-binding protein from Escherichia coli
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Holck, A., primary, Lossius, I., additional, Aasland, R., additional, and Kleppe, K., additional
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- 1987
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24. An efficient manual method for aligning DNA restriction map data on very large genomic restriction maps
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Aasland, R., primary and Smith, C. L., additional
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- 1988
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25. Identity of the 17-kilodalton protein, a DNA-binding protein from Escherichia coli, and the firA gene product
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Aasland, R, primary, Coleman, J, additional, Holck, A L, additional, Smith, C L, additional, Raetz, C R, additional, and Kleppe, K, additional
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- 1988
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26. Economic incentives for military housing residents to conserve utilities. Master's thesis
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Aasland, R
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- 1992
27. ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
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Allegra Via, Chenna Ramu, Ivica Letunic, David M. A. Martin, Caroline McGuigan, Pål Puntervoll, Scott Cameron, Sophie Chabanis-Davidson, Gabriele Ausiello, Bernhard Kuster, Toby J. Gibson, Christine Gemünd, Anna Costantini, Manuela Helmer-Citterich, Giulio Superti-Furga, Rune Linding, Francesca Diella, Barbara Brannetti, Gianni Cesareni, Rein Aasland, Morten Mattingsdal, Leszek Rychlewski, Rambabu Gudavalli, Lucjan Wyrwicz, William N. Hunter, Peer Bork, Fabrizio Ferrè, Vincenza Maselli, Puntervoll P., Linding R., Gemund C., Chabanis-Davidson S., Mattingsdal M., Cameron S., Martin D.M.A., Ausiello G., Brannetti B., Costantini A., Ferrè Fabrizio., Maselli Vincenza, Via A., Cesareni G., Diella F., Superti-Furga G., Wyrwicz L., Ramu C., McGuigan C., Gudavalli R., Letunic I., Bork P., Rychlewski L., Kuster B., Helmer-Citterich M., Hunter W.N., Aasland R., Gibson T.J., and MDC Library
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Protein Structure ,Glycosylation ,Amino Acid Motifs ,Protein Sequence Analysis ,570 Life Sciences ,Computational biology ,macromolecular substances ,Eukaryotic Cell ,Biology ,Bioinformatics ,Domain (software engineering) ,610 Medical Sciences, Medicine ,chemistry.chemical_compound ,User-Computer Interface ,Sequence Analysis, Protein ,Genetics ,Compartment (development) ,Short linear motif ,Tertiary Protein Structure ,Sequence (medicine) ,Internet ,Settore BIO/11 ,Protein ,Protein Structure, Tertiary ,Proteins ,Software ,Eukaryotic Cells ,Articles ,Eukaryotic Linear Motif resource ,chemistry ,Cardiovascular and Metabolic Diseases ,Proteome ,Amino Acid Motif ,Sequence Analysis ,Function (biology) ,Tertiary - Abstract
Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line resources are available for revealing globular domains in sequences, there has hitherto been no comprehensive collection of small functional sites/ motifs comparable to the globular domain resources, yet these are as important for the function of multidomain proteins. Short linear peptide motifs are used for cell compartment targeting, protein–protein interaction, regulation by phosphorylation, acetylation, glycosylation and a host of other post-translational modifications. ELM, the Eukaryotic Linear Motif server at http://elm.eu.org/, is a new bioinformatics resource for investigating candidate short nonglobular functional motifs in eukaryotic proteins, aiming to fill the void in bioinformatics tools. Sequence comparisons with short motifs are difficult to evaluate because the usual significance assessments are inappropriate. Therefore the server is implemented with several logical filters to eliminate false positives. Current filters are for cell compartment, globular domain clash and taxonomic range. In favourable cases, the filters can reduce the number of retained matches by an order of magnitude or more.
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- 2003
28. Binding Specificity of ASHH2 CW Domain Toward H3K4me1 Ligand Is Coupled to Its Structural Stability Through Its α1-Helix.
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Bril'kov MS, Dobrovolska O, Ødegård-Fougner Ø, Turcu DC, Strømland Ø, Underhaug J, Aasland R, and Halskau Ø
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The CW domain binds to histone tail modifications found in different protein families involved in epigenetic regulation and chromatin remodeling. CW domains recognize the methylation state of the fourth lysine on histone 3 and could, therefore, be viewed as a reader of epigenetic information. The specificity toward different methylation states such as me1, me2, or me3 depends on the particular CW subtype. For example, the CW domain of ASHH2 methyltransferase binds preferentially to H3K4me1, and MORC3 binds to both H3K4me2 and me3 modifications, while ZCWPW1 is more specific to H3K4me3. The structural basis for these preferential bindings is not well understood, and recent research suggests that a more complete picture will emerge if dynamical and energetic assessments are included in the analysis of interactions. This study uses fold assessment by NMR in combination with mutagenesis, ITC affinity measurements, and thermal denaturation studies to investigate possible couplings between ASHH2 CW selectivity toward H3K4me1 and the stabilization of the domain and loops implicated in binding. The key elements of the binding site-the two tryptophans and the α1-helix form and maintain the binding pocket- were perturbed by mutagenesis and investigated. Results show that the α1-helix maintains the overall stability of the fold via the I915 and L919 residues and that the correct binding consolidates the loops designated as η1 and η3, as well as the C-terminal. This consolidation is incomplete for H3K4me3 binding to CW, which experiences a decrease in overall thermal stability on binding. Loop mutations not directly involved in the binding site, nonetheless, affect the equilibrium positions of the key residues., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Bril’kov, Dobrovolska, Ødegård-Fougner, Turcu, Strømland, Underhaug, Aasland and Halskau.)
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- 2022
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29. The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection.
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Dobrovolska O, Brilkov M, Madeleine N, Ødegård-Fougner Ø, Strømland Ø, Martin SR, De Marco V, Christodoulou E, Teigen K, Isaksson J, Underhaug J, Reuter N, Aalen RB, Aasland R, and Halskau Ø
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- Binding Sites, Histone-Lysine N-Methyltransferase metabolism, Histones metabolism, Molecular Dynamics Simulation, Nuclear Magnetic Resonance, Biomolecular, Protein Conformation, Protein Processing, Post-Translational, Arabidopsis enzymology, Histone-Lysine N-Methyltransferase chemistry, Histones chemistry
- Abstract
Chromatin post-translational modifications are thought to be important for epigenetic effects on gene expression. Methylation of histone N-terminal tail lysine residues constitutes one of many such modifications, executed by families of histone lysine methyltransferase (HKMTase). One such protein is ASHH2 from the flowering plant Arabidopsis thaliana, equipped with the interaction domain, CW, and the HKMTase domain, SET. The CW domain of ASHH2 is a selective binder of monomethylation at lysine 4 on histone H3 (H3K4me1) and likely helps the enzyme dock correctly onto chromatin sites. The study of CW and related interaction domains has so far been emphasizing lock-key models, missing important aspects of histone-tail CW interactions. We here present an analysis of the ASHH2 CW-H3K4me1 complex using NMR and molecular dynamics, as well as mutation and affinity studies of flexible coils. β-augmentation and rearrangement of coils coincide with changes in the flexibility of the complex, in particular the η1, η3 and C-terminal coils, but also in the β1 and β2 strands and the C-terminal part of the ligand. Furthermore, we show that mutating residues with outlier dynamic behaviour affect the complex binding affinity despite these not being in direct contact with the ligand. Overall, the binding process is consistent with conformational selection. We propose that this binding mechanism presents an advantage when searching for the correct post-translational modification state among the highly modified and flexible histone tails, and also that the binding shifts the catalytic SET domain towards the nucleosome. DATABASES: Structural data are available in the PDB database under the accession code 6QXZ. Resonance assignments for CW42 in its apo- and holo-forms are available in the BMRB database under the accession code 27251., (© 2020 The Authors. The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.)
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- 2020
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30. 1 H, 13 C, and 15 N resonance assignments of CW domain of the N-methyltransferase ASHH2 free and bound to the mono-, di- and tri-methylated histone H3 tail peptides.
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Dobrovolska O, Bril'kov M, Ødegård-Fougner Ø, Aasland R, and Halskau Ø
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- Amino Acid Sequence, Methylation, Protein Binding, Histones chemistry, Histones metabolism, Methyltransferases chemistry, Methyltransferases metabolism, Nuclear Magnetic Resonance, Biomolecular
- Abstract
The ASHH2 CW domain is responsible for recognizing the methylation state at lysine 4 of histone 3 N-terminal tails and implicated in the recruitment of the ASHH2 methyltransferase enzyme correctly to the histones. The ASHH2 CW domain binds H3 lysine motifs that can be either mono-, di-, or tri-methylated [ARTK(meX)QTAR, where X denotes the number of methylations], but binds strongest to monomethylated instances (K
d values reported in the range of 1 µm to 500 nM). Hoppmann et al. published the uncomplexed NMR structure of an ASHH2 CW domain in 2011. Here we document the assignment of a shortened ASHH2 CW construct, CW42, with similar binding affinity and better expression yields than the one used to solve the uncomplexed structure. We also perform1 H-15 N HSQC-monitored titrations that document at which protein-peptide ratios the complex is saturated. Backbone resonance assignments are presented for this shortened ASHH2 CW domain alone and bound to an H3 histone tail mimicking peptide monomethylated on lysine 4 (ARTK(me1)QTAR). Likewise, the assignment was also performed for the protein in complex with the dimethylated (ARTK(me2)QTAR) and trimethylated (ARTK(me3)QTAR) peptide. Overall, these two latter situations displayed a similar perturbation of shifts as the mono-methylated instance. In the case of the monomethylated histone tail mimic, side-chain assignment of CW42 in this complex was performed and reported in addition to backbone assignment, in preparation of a future solution structure determination and dynamics characterization of the CW42-ARTK(me1)QTAR complex.- Published
- 2018
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31. Proteolytic activity assayed by subcellular localization switching of a substrate.
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Szilvay AM, Sarria SV, Mannelqvist M, Aasland R, and Furnes C
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An approach to assay proteolytic activity in vivo by altering the subcellular localization of a labelled substrate was demonstrated. The assay included a protein shuttling between different cellular compartments and a site-specific recombinant protease. The shuttle protein used was the human immunodeficiency virus type 1 (HIV-1) Rev protein tandemly fused to the enhanced green fluorescent protein (EGFP) and the red fluorescent protein (RFP), while the protease was the site-specific protease VP24 from the herpes simplex virus type 1 (HSV-1). The fluorescent proteins in the Rev fusion protein were separated by a cleavage site specific for the VP24 protease. When co-expressed in COS-7 cells proteolysis was observed by fluorescence microscopy as a shift from a predominantly cytoplasmic localization of the fusion protein RevEGFP to a nuclear localization while the RFP part of the fusion protein remained in the cytoplasm. The cleavage of the fusion protein by VP24 was confirmed by Western blot analysis. The activity of VP24, when tagged N-terminally by the Myc-epitope, was found to be comparable to VP24. These results demonstrates that the activity and localization of a recombinantly expressed protease can be assessed by protease-mediated cleavage of fusion proteins containing a specific protease cleavage site.
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- 2016
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32. Towards Rational Design of a Toxoid Vaccine against the Heat-Stable Toxin of Escherichia coli.
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Taxt AM, Diaz Y, Aasland R, Clements JD, Nataro JP, Sommerfelt H, and Puntervoll P
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- Antibodies, Monoclonal, Cell Line, Tumor, Drug Design, Enzyme-Linked Immunosorbent Assay methods, Epitopes, Humans, Models, Molecular, Mutagenesis, Protein Conformation, Bacterial Toxins immunology, Enterotoxins immunology, Escherichia coli metabolism, Escherichia coli Infections prevention & control, Escherichia coli Proteins immunology, Escherichia coli Vaccines immunology, Toxoids immunology
- Abstract
Enterotoxigenic Escherichia coli(ETEC) is an important cause of diarrheal disease and death in children <5 years old. ETEC strains that express the heat-stable toxin (ST), with or without the heat-labile toxin, are among the four most important diarrhea-causing pathogens. This makes ST an attractive target for an ETEC vaccine. An ST vaccine should be nontoxic and elicit an immune response that neutralizes native ST without cross-reacting with the human endogenous guanylate cyclase C receptor ligands. To identify variants of ST with no or low toxicity, we screened a library of all 361 possible single-amino-acid mutant forms of ST by using the T84 cell assay. Moreover, we identified mutant variants with intact epitopes by screening for the ability to bind neutralizing anti-ST antibodies. ST mutant forms with no or low toxicity and intact epitopes are termed toxoid candidates, and the top 30 candidates all had mutations of residues A14, N12, and L9. The identification of nontoxic variants of L9 strongly suggests that it is a novel receptor-interacting residue, in addition to the previously identified N12, P13, and A14 residues. The screens also allowed us to map the epitopes of three neutralizing monoclonal antibodies, one of which cross-reacts with the human ligand uroguanylin. The common dominant epitope residue for all non-cross-reacting antibodies was Y19. Our results suggest that it should be possible to rationally design ST toxoids that elicit neutralizing immune responses against ST with minimal risk of immunological cross-reactivity., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)
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- 2016
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33. The PHD finger of p300 influences its ability to acetylate histone and non-histone targets.
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Rack JGM, Lutter T, Kjæreng Bjerga GE, Guder C, Ehrhardt C, Värv S, Ziegler M, and Aasland R
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- Acetylation, Binding Sites genetics, Biocatalysis, E1A-Associated p300 Protein genetics, HEK293 Cells, HeLa Cells, Humans, Immunoblotting, Immunohistochemistry, Microscopy, Fluorescence, Models, Molecular, Point Mutation, Protein Binding, E1A-Associated p300 Protein chemistry, E1A-Associated p300 Protein metabolism, Histones metabolism, Protein Structure, Tertiary
- Abstract
In enzymes that regulate chromatin structure, the combinatorial occurrence of modules that alter and recognise histone modifications is a recurrent feature. In this study, we explored the functional relationship between the acetyltransferase domain and the adjacent bromodomain/PHD finger (bromo/PHD) region of the transcriptional coactivator p300. We found that the bromo/PHD region of p300 can bind to the acetylated catalytic domain in vitro and augment the catalytic activity of the enzyme. Deletion of the PHD finger, but not the bromodomain, impaired the ability of the enzyme to acetylate histones in vivo, whilst it enhanced p300 self-acetylation. A point mutation in the p300 PHD finger that is related to the Rubinstein-Taybi syndrome resulted in increased self-acetylation but retained the ability to acetylate histones. Hence, the PHD finger appears to negatively regulate self-acetylation. Furthermore, our data suggest that the PHD finger has a role in the recruitment of p300 to chromatin., (Copyright © 2014 Elsevier Ltd. All rights reserved.)
- Published
- 2014
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34. Characterization of immunological cross-reactivity between enterotoxigenic Escherichia coli heat-stable toxin and human guanylin and uroguanylin.
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Taxt AM, Diaz Y, Bacle A, Grauffel C, Reuter N, Aasland R, Sommerfelt H, and Puntervoll P
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- Amino Acid Sequence, Animals, Bacterial Toxins chemistry, Bacterial Toxins genetics, Bacterial Toxins immunology, Cloning, Molecular, Enterotoxigenic Escherichia coli genetics, Enterotoxins chemistry, Enterotoxins genetics, Enterotoxins immunology, Escherichia coli Proteins chemistry, Escherichia coli Proteins genetics, Escherichia coli Proteins immunology, Gastrointestinal Hormones chemistry, Gastrointestinal Hormones genetics, Gastrointestinal Hormones immunology, Gene Expression Regulation, Bacterial immunology, Humans, Models, Molecular, Natriuretic Peptides chemistry, Natriuretic Peptides genetics, Natriuretic Peptides immunology, Protein Binding, Protein Conformation, Bacterial Toxins metabolism, Enterotoxigenic Escherichia coli metabolism, Enterotoxins metabolism, Escherichia coli Proteins metabolism, Gastrointestinal Hormones metabolism, Natriuretic Peptides metabolism
- Abstract
Enterotoxigenic Escherichia coli (ETEC) expressing the heat-stable toxin (ST) (human-type [STh] and porcine-type [STp] variants) is among the five most important enteric pathogens in young children living in low- and middle-income countries. ST mediates diarrheal disease through activation of the guanylate cyclase C (GC-C) receptor and is an attractive vaccine target with the potential to confer protection against a wide range of ETEC strains. However, immunological cross-reactivity to the endogenous GC-C ligands guanylin and uroguanylin is a major concern because of the similarities to ST in amino acid sequence, structure, and function. We have investigated the presence of similar epitopes on STh, STp, guanylin, and uroguanylin by analyzing these peptides in eight distinct competitive enzyme-linked immunosorbent assays (ELISAs). A fraction (27%) of a polyclonal anti-STh antibody and an anti-STh monoclonal antibody (MAb) cross-reacted with uroguanylin, the latter with a 73-fold-lower affinity. In contrast, none of the antibodies raised against STp, one polyclonal antibody and three MAbs, cross-reacted with the endogenous peptides. Antibodies raised against guanylin and uroguanylin showed partial cross-reactivity with the ST peptides. Our results demonstrate, for the first time, that immunological cross-reactions between ST and the endogenous peptides can occur. However, the partial nature and low affinity of the observed cross-reactions suggest that the risk of adverse effects from a future ST vaccine may be low. Furthermore, our results suggest that this risk may be reduced or eliminated by basing an ST immunogen on STp or a selectively mutated variant of STh., (Copyright © 2014, American Society for Microbiology. All Rights Reserved.)
- Published
- 2014
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35. Constitutive nuclear localization of an alternatively spliced sirtuin-2 isoform.
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Rack JG, VanLinden MR, Lutter T, Aasland R, and Ziegler M
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- 5' Untranslated Regions, Alternative Splicing, Catalytic Domain genetics, Cell Nucleus enzymology, HEK293 Cells, HeLa Cells, Humans, Models, Molecular, Nuclear Export Signals, Protein Conformation, Protein Folding, Protein Isoforms chemistry, Protein Isoforms genetics, Protein Isoforms metabolism, Protein Structure, Tertiary, RNA Precursors genetics, RNA Precursors metabolism, Recombinant Proteins chemistry, Recombinant Proteins genetics, Recombinant Proteins metabolism, Sirtuin 2 chemistry, Static Electricity, Sirtuin 2 genetics, Sirtuin 2 metabolism
- Abstract
Sirtuin-2 (SIRT2), the cytoplasmic member of the sirtuin family, has been implicated in the deacetylation of nuclear proteins. Although the enzyme has been reported to be located to the nucleus during G2/M phase, its spectrum of targets suggests functions in the nucleus throughout the cell cycle. While a nucleocytoplasmic shuttling mechanism has been proposed for SIRT2, recent studies have indicated the presence of a constitutively nuclear isoform. Here we report the identification of a novel splice variant (isoform 5) of SIRT2 that lacks a nuclear export signal and encodes a predominantly nuclear isoform. This novel isoform 5 fails to show deacetylase activity using several assays, both in vitro and in vivo, and we are led to conclude that this isoform is catalytically inactive. Nevertheless, it retains the ability to interact with p300, a known interaction partner. Moreover, changes in intrinsic tryptophan fluorescence upon denaturation indicate that the protein is properly folded. These data, together with computational analyses, confirm the structural integrity of the catalytic domain. Our results suggest an activity-independent nuclear function of the novel isoform., (© 2013.)
- Published
- 2014
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36. The CW domain, a new histone recognition module in chromatin proteins.
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Hoppmann V, Thorstensen T, Kristiansen PE, Veiseth SV, Rahman MA, Finne K, Aalen RB, and Aasland R
- Subjects
- Arabidopsis metabolism, Gene Expression Profiling, Gene Expression Regulation, Histone Methyltransferases, Histone-Lysine N-Methyltransferase metabolism, Histones metabolism, Methylation, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Protein Binding, Protein Interaction Mapping, Protein Structure, Tertiary, Surface Plasmon Resonance, Arabidopsis chemistry, Histone-Lysine N-Methyltransferase chemistry, Protein Interaction Domains and Motifs
- Abstract
Post-translational modifications of the N-terminal histone tails, including lysine methylation, have key roles in regulation of chromatin and gene expression. A number of protein modules have been identified that recognize differentially modified histone tails and provide their proteins with the capacity to sense such modifications. Here, we identify the CW domain of plant and animal chromatin-related proteins as a novel module that recognizes different methylated states of lysine 4 on histone H3 (H3K4me). The solution structure of the CW domain of the Arabidopsis ASH1 HOMOLOG2 (ASHH2) histone methyltransferase provides insight into how different CW domains can distinguish different methylated histone tails. We provide evidence that ASHH2 is acting on H3K4me-marked genes, allowing for ASHH2-dependent H3K36 tri-methylation, which contributes to sustained expression of tissue-specific and developmentally regulated genes. This suggests that ASHH2 is a combined 'reader' and 'writer' of the histone code. We propose that different CW domains, dependent on their specificity for different H3K4 methylations, are important for epigenetic memory or participate in switching between permissive and repressive chromatin states.
- Published
- 2011
- Full Text
- View/download PDF
37. Structure of mammalian AMPK and its regulation by ADP.
- Author
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Xiao B, Sanders MJ, Underwood E, Heath R, Mayer FV, Carmena D, Jing C, Walker PA, Eccleston JF, Haire LF, Saiu P, Howell SA, Aasland R, Martin SR, Carling D, and Gamblin SJ
- Subjects
- AMP-Activated Protein Kinases genetics, Adenosine Monophosphate metabolism, Adenosine Monophosphate pharmacology, Adenosine Triphosphate metabolism, Adenosine Triphosphate pharmacology, Allosteric Regulation drug effects, Allosteric Regulation genetics, Animals, Binding Sites, Crystallography, X-Ray, Enzyme Activation drug effects, Enzyme Activation genetics, Kinetics, Magnesium metabolism, Mammals, Models, Molecular, Phosphorylation drug effects, Phosphorylation genetics, Protein Binding, Protein Structure, Tertiary drug effects, Protein Structure, Tertiary genetics, Thermodynamics, AMP-Activated Protein Kinases chemistry, AMP-Activated Protein Kinases metabolism, Adenosine Diphosphate metabolism, Adenosine Diphosphate pharmacology
- Abstract
The heterotrimeric AMP-activated protein kinase (AMPK) has a key role in regulating cellular energy metabolism; in response to a fall in intracellular ATP levels it activates energy-producing pathways and inhibits energy-consuming processes. AMPK has been implicated in a number of diseases related to energy metabolism including type 2 diabetes, obesity and, most recently, cancer. AMPK is converted from an inactive form to a catalytically competent form by phosphorylation of the activation loop within the kinase domain: AMP binding to the γ-regulatory domain promotes phosphorylation by the upstream kinase, protects the enzyme against dephosphorylation, as well as causing allosteric activation. Here we show that ADP binding to just one of the two exchangeable AXP (AMP/ADP/ATP) binding sites on the regulatory domain protects the enzyme from dephosphorylation, although it does not lead to allosteric activation. Our studies show that active mammalian AMPK displays significantly tighter binding to ADP than to Mg-ATP, explaining how the enzyme is regulated under physiological conditions where the concentration of Mg-ATP is higher than that of ADP and much higher than that of AMP. We have determined the crystal structure of an active AMPK complex. The structure shows how the activation loop of the kinase domain is stabilized by the regulatory domain and how the kinase linker region interacts with the regulatory nucleotide-binding site that mediates protection against dephosphorylation. From our biochemical and structural data we develop a model for how the energy status of a cell regulates AMPK activity.
- Published
- 2011
- Full Text
- View/download PDF
38. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate.
- Author
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Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Cañestro C, Bouquet JM, Danks G, Poulain J, Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S, Tsagkogeorga G, Konrad A, Singh S, Jensen MF, Huynh Cong E, Eikeseth-Otteraa H, Noel B, Anthouard V, Porcel BM, Kachouri-Lafond R, Nishino A, Ugolini M, Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, Reinhardt R, Weissenbach J, Roy SW, Artiguenave F, Postlethwait JH, Manak JR, Thompson EM, Jaillon O, Du Pasquier L, Boudinot P, Liberles DA, Volff JN, Philippe H, Lenhard B, Roest Crollius H, Wincker P, and Chourrout D
- Subjects
- Animals, DNA Transposable Elements, DNA, Intergenic, Exons, Gene Order, Genes, Duplicate, Genes, Homeobox, Introns, Invertebrates classification, Invertebrates genetics, Molecular Sequence Data, Recombination, Genetic, Spliceosomes metabolism, Synteny, Urochordata anatomy & histology, Urochordata classification, Urochordata immunology, Vertebrates classification, Vertebrates genetics, Biological Evolution, Genome, Urochordata genetics
- Abstract
Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.
- Published
- 2010
- Full Text
- View/download PDF
39. Reading, writing and editing methylated lysines on histone tails: new insights from recent structural studies.
- Author
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Justin N, De Marco V, Aasland R, and Gamblin SJ
- Subjects
- Animals, Humans, Jumonji Domain-Containing Histone Demethylases metabolism, Methylation, Epistasis, Genetic, Histones chemistry, Histones metabolism, Lysine metabolism
- Abstract
The phenotypes of different cell types are governed by their differential gene expression programmes, which are prominently influenced by epigenetic gene regulation featuring heritable chromatin states. Different epigenetic states are associated with distinctive patterns of post-translational modifications of the histone tails, which in turn influence the recruitment of chromatin-modifying effectors and local chromatin structure. Despite rapid advances in understanding how particular histone marks correlate with transcriptional output, many of the molecular details on how the maintenance and alteration of these modifications relate to fundamental processes such as replication, DNA repair, and transcription remain to be elucidated. Here, we review recent advances in the structural description of the reading, writing, and editing of two histone methylation marks with opposite functions: at histone H3 lysine 4 (H3K4)-associated with actively transcribed genes, and at histone H3 lysine 27 (H3K27)-a hallmark of silenced chromatin. These two marks are associated with trithorax and polycomb, respectively, prototypes of the genes involved in epigenetic inheritance in Drosophila. We also briefly discuss some recent examples of how the readout of particular marks is influenced by the presence of other modifications., (Copyright © 2010 Elsevier Ltd. All rights reserved.)
- Published
- 2010
- Full Text
- View/download PDF
40. Heat-stable enterotoxin of enterotoxigenic Escherichia coli as a vaccine target.
- Author
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Taxt A, Aasland R, Sommerfelt H, Nataro J, and Puntervoll P
- Subjects
- Amino Acid Sequence, Bacterial Toxins toxicity, Enterotoxins toxicity, Escherichia coli Proteins, Escherichia coli Vaccines adverse effects, Humans, Models, Molecular, Molecular Sequence Data, Protein Structure, Tertiary, Bacterial Toxins immunology, Enterotoxigenic Escherichia coli immunology, Enterotoxins immunology, Escherichia coli Vaccines immunology
- Abstract
Enterotoxigenic Escherichia coli (ETEC) is responsible for 280 million to 400 million episodes of diarrhea and about 380,000 deaths annually. Epidemiological data suggest that ETEC strains which secrete heat-stable toxin (ST), alone or in combination with heat-labile toxin (LT), induce the most severe disease among children in developing countries. This makes ST an attractive target for inclusion in an ETEC vaccine. ST is released upon colonization of the small intestine and activates the guanylate cyclase C receptor, causing profuse diarrhea. To generate a successful toxoid, ST must be made immunogenic and nontoxic. Due to its small size, ST is nonimmunogenic in its natural form but becomes immunogenic when coupled to an appropriate large-molecular-weight carrier. This has been successfully achieved with several carriers, using either chemical conjugation or recombinant fusion techniques. Coupling of ST to a carrier may reduce toxicity, but further reduction by mutagenesis is desired to obtain a safe vaccine. More than 30 ST mutants with effects on toxicity have been reported. Some of these mutants, however, have lost the ability to elicit neutralizing immune responses to the native toxin. Due to the small size of ST, separating toxicity from antigenicity is a particular challenge that must be met. Another obstacle to vaccine development is possible cross-reactivity between anti-ST antibodies and the endogenous ligands guanylin and uroguanylin, caused by structural similarity to ST. Here we review the molecular and biological properties of ST and discuss strategies for developing an ETEC vaccine that incorporates immunogenic and nontoxic derivatives of the ST toxin.
- Published
- 2010
- Full Text
- View/download PDF
41. ELM: the status of the 2010 eukaryotic linear motif resource.
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Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Helmer-Citterich M, Linding R, and Gibson TJ
- Subjects
- Amino Acid Sequence, Animals, Computational Biology trends, Databases, Protein, Humans, Information Storage and Retrieval methods, Internet, Molecular Sequence Data, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Software, Amino Acid Motifs genetics, Computational Biology methods, Databases, Genetic, Databases, Nucleic Acid, Eukaryotic Cells chemistry
- Abstract
Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. Many thousands of linear motif instances, most notably phosphorylation sites, have now been reported. Although clearly very abundant, linear motifs are difficult to predict de novo in protein sequences due to the difficulty of obtaining robust statistical assessments. The ELM resource at http://elm.eu.org/ provides an expanding knowledge base, currently covering 146 known motifs, with annotation that includes >1300 experimentally reported instances. ELM is also an exploratory tool for suggesting new candidates of known linear motifs in proteins of interest. Information about protein domains, protein structure and native disorder, cellular and taxonomic contexts is used to reduce or deprecate false positive matches. Results are graphically displayed in a 'Bar Code' format, which also displays known instances from homologous proteins through a novel 'Instance Mapper' protocol based on PHI-BLAST. ELM server output provides links to the ELM annotation as well as to a number of remote resources. Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation.
- Published
- 2010
- Full Text
- View/download PDF
42. The Schizosaccharomyces pombe JmjC-protein, Msc1, prevents H2A.Z localization in centromeric and subtelomeric chromatin domains.
- Author
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Buchanan L, Durand-Dubief M, Roguev A, Sakalar C, Wilhelm B, Strålfors A, Shevchenko A, Aasland R, Shevchenko A, Ekwall K, and Francis Stewart A
- Subjects
- Acetylation, Adenosine Triphosphatases, Amino Acid Sequence, DNA, Intergenic, DNA-Binding Proteins genetics, Gene Silencing, Lysine metabolism, Models, Biological, Molecular Chaperones metabolism, Molecular Sequence Data, Protein Subunits, Saccharomyces cerevisiae Proteins, Schizosaccharomyces pombe Proteins genetics, Sequence Homology, Amino Acid, Chromosome Structures metabolism, DNA-Binding Proteins metabolism, Histones metabolism, Proteomics methods, Schizosaccharomyces genetics, Schizosaccharomyces pombe Proteins metabolism
- Abstract
Eukaryotic genomes are repetitively packaged into chromatin by nucleosomes, however they are regulated by the differences between nucleosomes, which establish various chromatin states. Local chromatin cues direct the inheritance and propagation of chromatin status via self-reinforcing epigenetic mechanisms. Replication-independent histone exchange could potentially perturb chromatin status if histone exchange chaperones, such as Swr1C, loaded histone variants into wrong sites. Here we show that in Schizosaccharomyces pombe, like Saccharomyces cerevisiae, Swr1C is required for loading H2A.Z into specific sites, including the promoters of lowly expressed genes. However S. pombe Swr1C has an extra subunit, Msc1, which is a JumonjiC-domain protein of the Lid/Jarid1 family. Deletion of Msc1 did not disrupt the S. pombe Swr1C or its ability to bind and load H2A.Z into euchromatin, however H2A.Z was ectopically found in the inner centromere and in subtelomeric chromatin. Normally this subtelomeric region not only lacks H2A.Z but also shows uniformly lower levels of H3K4me2, H4K5, and K12 acetylation than euchromatin and disproportionately contains the most lowly expressed genes during vegetative growth, including many meiotic-specific genes. Genes within and adjacent to subtelomeric chromatin become overexpressed in the absence of either Msc1, Swr1, or paradoxically H2A.Z itself. We also show that H2A.Z is N-terminally acetylated before, and lysine acetylated after, loading into chromatin and that it physically associates with the Nap1 histone chaperone. However, we find a negative correlation between the genomic distributions of H2A.Z and Nap1/Hrp1/Hrp3, suggesting that the Nap1 chaperones remove H2A.Z from chromatin. These data describe H2A.Z action in S. pombe and identify a new mode of chromatin surveillance and maintenance based on negative regulation of histone variant misincorporation., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2009
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- View/download PDF
43. The Arabidopsis SET-domain protein ASHR3 is involved in stamen development and interacts with the bHLH transcription factor ABORTED MICROSPORES (AMS).
- Author
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Thorstensen T, Grini PE, Mercy IS, Alm V, Erdal S, Aasland R, and Aalen RB
- Subjects
- Amino Acid Sequence, Arabidopsis Proteins chemistry, Arabidopsis Proteins metabolism, Base Sequence, DNA Primers, HeLa Cells, Humans, Molecular Sequence Data, Protein Binding, Sequence Homology, Amino Acid, Two-Hybrid System Techniques, Arabidopsis growth & development, Arabidopsis Proteins physiology, Basic Helix-Loop-Helix Transcription Factors metabolism
- Abstract
The Arabidopsis thaliana genome contains more than 30 genes encoding SET-domain proteins that are thought to be epigenetic regulators of gene expression and chromatin structure. SET-domain proteins can be divided into subgroups, and members of the Polycomb group (PcG) and trithorax group (trxG) have been shown to be important regulators of development. Both in animals and plants some of these proteins are components of multimeric protein complexes. Here, we have analyzed the Arabidopsis trxG protein ASHR3 which has a SET domain and pre- and post-SET domains similar to that of Ash1 in Drosophila. In addition to the SET domain, a divergent PHD finger is found in the N-terminus of the ASHR3 protein. As expected from SET-domain proteins involved in transcriptional activation, ASHR3 (coupled to GFP) localizes to euchromatin. A yeast two-hybrid screening revealed that the ASHR3 protein interacts with the putative basic helix-loop-helix (bHLH) transcription factor ABORTED MICROSPORES (AMS), which is involved in anther and stamen development in Arabidopsis. Deletion mapping indicated that both the PHD finger and the SET domain mediate the interaction between the two proteins. Overexpression of ASHR3 led in general to growth arrest, and specifically to degenerated anthers and male sterility. Expression analyses demonstrated that ASHR3 like AMS is expressed in the anther and in stamen filaments. We therefore propose that AMS can target ASHR3 to chromatin and regulate genes involved in stamen development and function.
- Published
- 2008
- Full Text
- View/download PDF
44. Using hydropathy features for function prediction of membrane proteins.
- Author
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Pánek J, Eidhammer I, and Aasland R
- Subjects
- Amino Acid Sequence, Carrier Proteins, Computational Biology, Membrane Proteins, Proteins physiology, Hydrophobic and Hydrophilic Interactions, Models, Molecular, Proteins chemistry
- Abstract
A novel alignment-free method for computing functional similarity of membrane proteins based on features of hydropathy distribution is presented. The features of hydropathy distribution are used to represent protein families as hydropathy profiles. The profiles statistically summarize the hydropathy distribution of member proteins. The summation is made by using hydropathy features that numerically represent structurally/functionally significant portions of protein sequences. The hydropathy profiles are numerical vectors that are points in a high dimensional 'hydropathy' space. Their similarities are identified by projection of the space onto principal axes. Here, the approach is applied to the secondary transporters. The analysis using the presented approach is validated by the standard classification of the secondary transporters. The presented analysis allows for prediction of function attributes for proteins of uncharacterized families of secondary transporters. The results obtained using the presented analysis may help to characterize unknown function attributes of secondary transporters. They also show that analysis of hydropathy distribution can be used for function prediction of membrane proteins.
- Published
- 2007
- Full Text
- View/download PDF
45. Multiple epigenetic maintenance factors implicated by the loss of Mll2 in mouse development.
- Author
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Glaser S, Schaft J, Lubitz S, Vintersten K, van der Hoeven F, Tufteland KR, Aasland R, Anastassiadis K, Ang SL, and Stewart AF
- Subjects
- Alleles, Animals, Apoptosis genetics, Cell Line, Female, Fetal Growth Retardation genetics, Gene Expression Regulation, Developmental physiology, Genes, Lethal, Histone-Lysine N-Methyltransferase, Mice, Mice, Knockout, Mice, Transgenic, Myeloid-Lymphoid Leukemia Protein physiology, Phenotype, Epigenesis, Genetic physiology, Gene Deletion, Myeloid-Lymphoid Leukemia Protein deficiency, Myeloid-Lymphoid Leukemia Protein genetics
- Abstract
Epigenesis is the process whereby the daughters of a dividing cell retain a chromatin state determined before cell division. The best-studied cases involve the inheritance of heterochromatic chromosomal domains, and little is known about specific gene regulation by epigenetic mechanisms. Recent evidence shows that epigenesis pivots on methylation of nucleosomes at histone 3 lysines 4, 9 or 27. Bioinformatics indicates that mammals have several enzymes for each of these methylations, including at least six histone 3 lysine 4 methyltransferases. To look for evidence of gene-specific epigenetic regulation in mammalian development, we examined one of these six, Mll2, using a multipurpose allele in the mouse to ascertain the loss-of-function phenotype. Loss of Mll2 slowed growth, increased apoptosis and retarded development, leading to embryonic failure before E11.5. Using chimera experiments, we demonstrated that Mll2 is cell-autonomously required. Evidence for gene-specific regulation was also observed. Although Mox1 and Hoxb1 expression patterns were correctly established, they were not maintained in the absence of Mll2, whereas Wnt1 and Otx2 were. The Mll2 loss-of-function phenotype is different from that of its sister gene Mll, and they regulate different Hox complex genes during ES cell differentiation. Therefore, these two closely related epigenetic factors play different roles in development and maintain distinct gene expression patterns. This suggests that other epigenetic factors also regulate particular patterns and that development entails networks of epigenetic specificities.
- Published
- 2006
- Full Text
- View/download PDF
46. Eap45 in mammalian ESCRT-II binds ubiquitin via a phosphoinositide-interacting GLUE domain.
- Author
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Slagsvold T, Aasland R, Hirano S, Bache KG, Raiborg C, Trambaiolo D, Wakatsuki S, and Stenmark H
- Subjects
- Amino Acid Sequence, Animals, Binding Sites, Carrier Proteins chemistry, Carrier Proteins genetics, Carrier Proteins metabolism, DNA-Binding Proteins genetics, Endosomal Sorting Complexes Required for Transport, Endosomes metabolism, HeLa Cells, Humans, In Vitro Techniques, Membrane Transport Proteins chemistry, Membrane Transport Proteins genetics, Membrane Transport Proteins metabolism, Mice, Models, Molecular, Molecular Sequence Data, Multiprotein Complexes, Protein Binding, Protein Structure, Tertiary, Recombinant Proteins chemistry, Recombinant Proteins genetics, Recombinant Proteins metabolism, Saccharomyces cerevisiae Proteins chemistry, Saccharomyces cerevisiae Proteins genetics, Saccharomyces cerevisiae Proteins metabolism, Sequence Homology, Amino Acid, Transcription Factors genetics, Vesicular Transport Proteins, DNA-Binding Proteins chemistry, DNA-Binding Proteins metabolism, Transcription Factors chemistry, Transcription Factors metabolism, Ubiquitin metabolism
- Abstract
Ubiquitination serves as a key sorting signal in the lysosomal degradation of endocytosed receptors through the ability of ubiquitinated membrane proteins to be recognized and sorted by ubiquitin-binding proteins along the endocytic route. The ESCRT-II complex in yeast contains one such protein, Vps36, which harbors a ubiquitin-binding NZF domain and is required for vacuolar sorting of ubiquitinated membrane proteins. Surprisingly, the presumptive mammalian ortholog Eap45 lacks the ubiquitin-binding module of Vps36, and it is thus not clear whether mammalian ESCRT-II functions to bind ubiquitinated cargo. In this paper, we provide evidence that Eap45 contains a novel ubiquitin-binding domain, GLUE (GRAM-like ubiquitin-binding in Eap45), which binds ubiquitin with similar affinity and specificity as other ubiquitin-binding domains. The GLUE domain shares similarities in its primary and predicted secondary structures to phosphoinositide-binding GRAM and PH domains. Accordingly, we find that Eap45 binds to a subset of 3-phosphoinositides, suggesting that ubiquitin recognition could be coordinated with phosphoinositide binding. Furthermore, we show that Eap45 colocalizes with ubiquitinated proteins on late endosomes. These results are consistent with a role for Eap45 in endosomal sorting of ubiquitinated cargo.
- Published
- 2005
- Full Text
- View/download PDF
47. A new method for identification of protein (sub)families in a set of proteins based on hydropathy distribution in proteins.
- Author
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Pánek J, Eidhammer I, and Aasland R
- Subjects
- Algorithms, Amino Acid Sequence, Amino Acids chemistry, Cathepsins chemistry, Cell Membrane metabolism, Cluster Analysis, Databases, Protein, Models, Statistical, Molecular Sequence Data, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Sequence Alignment, Sequence Homology, Amino Acid, Membrane Proteins chemistry, Peptides chemistry, Proteins chemistry, Proteomics methods
- Abstract
Structural similarity among proteins is reflected in the distribution of hydropathicity along the amino acids in the protein sequence. Similarities in the hydropathy distributions are obvious for homologous proteins within a protein family. They also were observed for proteins with related structures, even when sequence similarities were undetectable. Here we present a novel method that employs the hydropathy distribution in proteins for identification of (sub)families in a set of (homologous) proteins. We represent proteins as points in a generalized hydropathy space, represented by vectors of specifically defined features. The features are derived from hydropathy of the individual amino acids. Projection of this space onto principal axes reveals groups of proteins with related hydropathy distributions. The groups identified correspond well to families of structurally and functionally related proteins. We found that this method accurately identifies protein families in a set of proteins, or subfamilies in a set of homologous proteins. Our results show that protein families can be identified by the analysis of hydropathy distribution, without the need for sequence alignment., (Copyright 2005 Wiley-Liss, Inc.)
- Published
- 2005
- Full Text
- View/download PDF
48. Functions for S. cerevisiae Swd2p in 3' end formation of specific mRNAs and snoRNAs and global histone 3 lysine 4 methylation.
- Author
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Dichtl B, Aasland R, and Keller W
- Subjects
- Amino Acid Sequence, Base Sequence, DNA, Fungal genetics, DNA-Binding Proteins genetics, DNA-Binding Proteins metabolism, Histone-Lysine N-Methyltransferase, Histones chemistry, Lysine chemistry, Macromolecular Substances, Methylation, Molecular Sequence Data, Multiprotein Complexes, RNA, Fungal chemistry, RNA, Fungal genetics, RNA, Messenger chemistry, RNA, Messenger genetics, RNA, Small Nucleolar chemistry, RNA, Small Nucleolar genetics, Repetitive Sequences, Amino Acid, Saccharomyces cerevisiae genetics, Saccharomyces cerevisiae metabolism, Saccharomyces cerevisiae Proteins genetics, Sequence Homology, Amino Acid, Transcription Factors genetics, Transcription Factors metabolism, mRNA Cleavage and Polyadenylation Factors genetics, mRNA Cleavage and Polyadenylation Factors metabolism, Histones metabolism, RNA, Fungal metabolism, RNA, Messenger metabolism, RNA, Small Nucleolar metabolism, Saccharomyces cerevisiae Proteins metabolism
- Abstract
The Saccharomyces cerevisiae WD-40 repeat protein Swd2p associates with two functionally distinct multiprotein complexes: the cleavage and polyadenylation factor (CPF) that is involved in pre-mRNA and snoRNA 3' end formation and the SET1 complex (SET1C) that methylates histone 3 lysine 4. Based on bioinformatic analysis we predict a seven-bladed beta-propeller structure for Swd2p proteins. Northern, transcriptional run-on and in vitro 3' end cleavage analyses suggest that temperature sensitive swd2 strains were defective in 3' end formation of specific mRNAs and snoRNAs. Protein-protein interaction studies support a role for Swd2p in the assembly of 3' end formation complexes. Furthermore, histone 3 lysine 4 di-and tri-methylation were adversely affected and telomeres were shortened in swd2 mutants. Underaccumulation of the Set1p methyltransferase accounts for the observed loss of SET1C activity and suggests a requirement for Swd2p for the stability or assembly of this complex. We also provide evidence that the roles of Swd2p as component of CPF and SET1C are functionally independent. Taken together, our results establish a dual requirement for Swd2p in 3' end formation and histone tail modification.
- Published
- 2004
- Full Text
- View/download PDF
49. Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300.
- Author
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Ragvin A, Valvatne H, Erdal S, Arskog V, Tufteland KR, Breen K, ØYan AM, Eberharter A, Gibson TJ, Becker PB, and Aasland R
- Subjects
- Histones metabolism, Humans, Protein Structure, Tertiary, Nuclear Proteins metabolism, Nucleosomes metabolism, Trans-Activators metabolism
- Abstract
The PHD finger and the bromodomain are small protein domains that occur in many proteins associated with phenomena related to chromatin. The bromodomain has been shown to bind acetylated lysine residues on histone tails. Lysine acetylation is one of several histone modifications that have been proposed to form the basis for a mechanism for recording epigenetically stable marks in chromatin, known as the histone code. The bromodomain is therefore thought to read a part of the histone code. Since PHD fingers often occur in proteins next to bromodomains, we have tested the hypothesis that the PHD finger can also interact with nucleosomes. Using two different in vitro assays, we found that the bromodomain/PHD finger region of the transcriptional cofactor p300 can bind to nucleosomes that have a high degree of histone acetylation. In a nucleosome retention assay, both domains were required for binding. Replacement of the p300 PHD finger with other PHD fingers resulted in loss of nucleosome binding. In an electrophoretic mobility shift assay, each domain alone showed, however, nucleosome-binding activity. The binding of the isolated PHD finger to nucleosomes was independent of the histone acetylation levels. Our data are consistent with a model where the two domains cooperate in nucleosome binding. In this model, both the bromodomain and the PHD finger contact the nucleosome while simultaneously interacting with each other.
- Published
- 2004
- Full Text
- View/download PDF
50. The many colours of chromodomains.
- Author
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Brehm A, Tufteland KR, Aasland R, and Becker PB
- Subjects
- Animals, Chromatin metabolism, Chromosomal Proteins, Non-Histone chemistry, Chromosomal Proteins, Non-Histone metabolism, DNA-Binding Proteins chemistry, DNA-Binding Proteins metabolism, Models, Molecular, Protein Conformation, Chromatin chemistry, Nucleic Acid Conformation
- Abstract
Local differences in chromatin organisation may profoundly affect the activity of eukaryotic genomes. Regulation at the level of DNA packaging requires the targeting of structural proteins and histone-modifying enzymes to specific sites and their stable or dynamic interaction with the nucleosomal fiber. The "chromodomain", a domain shared by many regulators of chromatin structure, has long been suspected to serve as a module mediating chromatin interactions in a variety of different protein contexts. However, recent functional analyses of a number of different chromodomains revealed an unexpected diversity of interaction targets, including histones, DNA and even RNA. The chromodomains of today seem to have evolved from a common ancestral fold to fulfill various functions in different molecular contexts. Combining information gained from recent functional and structural studies of chromodomains with a bioinformatic classification of their structure could lead to the definition of sequence motifs with predictive quality for chromodomain function., (Copyright 2004 Wiley Periodicals, Inc.)
- Published
- 2004
- Full Text
- View/download PDF
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