KAREN SKRIVER

RESEARCH

Protein-protein and protein-DNA interactions

Transcription factors control specific genes through molecular interactions and are regulated by ubiquitin-dependent degradation. We study the function of NAC transcription factors as regulators and regulatees, especially in the model plant Arabidopsis. This is an obvious model organism for studies of ubiquitin-dependent regulation of transcription factors and other regulatory proteins because of the over representation of ubiquitin components in this organism compared to other eukaryotes.

1) NAC transcription factors

We study the NAC transcription factors using protein chemistry, bioinformatics, and molecular biology. ANAC019, which is regulated by biotic and abiotic plant stress, was identified as an interaction partner of a RING E3 ubiquitin ligase in yeast two-hybrid screenings and its structure determined by x-ray crystallography in collaboration with Leila Lo Leggio. Target DNA-binding sequences were identified by binding site selection, and the binding mechanism was studied using EMSA assays and biosensor technology.

2) Regulated protein degradation

The U-box protein module is structurally related to the RING finger module. Both protein modules are present in E3 ubiquitin ligases which function in ubiquitin dependent degradation of regulatory proteins, such as the NAC transcription factors. We identify and examine interactions between E2 ubiquitin conjugating enzymes and E3 protein ligases and between E2 protein ligases and regulatory target proteins and use this information for targeted degradation by engineering.

CV – KAREN SKRIVER

Employment

93-      Associate professor, Department of Molecular Biology, University of Copenhagen

89-93  Staff scientist, Carlsberg Research Institute, Copenhagen

88-89  NIH international Fogarty fellow, Temple University School of Medicine, Philadelphia, laboratory of Prof. S.C. Bock

86-88  NIH international Fogarty fellow, The Rockefeller University, New York, laboratory of Prof. E.T. Kaiser and S.C. Bock.

84-86  Danish Cancer Society scholar, University of Århus, laboratory of Prof. Staffan Magnussen

Education

90        Ph.D. in biochemistry, University of Århus

86        Cand. scient. in chemistry and biology, University of Århus

Awards and grants

84-      Supported by: The Danish Cancer Society Scholarship Program, The NIH-International Fogarty Fellowship Program, The Danish Natural Science Research Council, The Danish Research Academy, The Danish Agricultural and Veterinary Research Council, The Plasmid Foundation, The Novo Nordisk Foundation, The Danish Research Agency.

98        Student elected teaching prize from The Faculty of Science, University of Copenhagen

Students & Teaching

93-      Responsible for the organization and teaching of courses in protein chemistry and protein biology at the bachelor and master levels.

            Currently supervisor for 8 masters students. Previously supervisor for 47 students who obtained their masters degree 95-07, and 5 students who obtained their Ph.D. degree 99-06

Others

07-      Candidate Study Board, The Faculty of Science, University of Copenhagen, member

06-      The Danish Research Council for Technology and Production, member

03        Sabbatical leave, laboratory of professor Nam-Hai Chua, The Rockefeller University, New York

02-07  Biochemistry study board, University of Copenhagen, board member.

00-      Referee for e.g. Biochemistry, Plant Mol. Biol., Plant Cell, Eur. J. Biochem., J. Biol. Chem., Nucleic Acids Res., Planta, Plant Cell Phys.

01-04  Danish Society for Biochemistry and Molecular Biology, board member

96-02  Institute of Molecular Biology, University of Copenhagen, board member

93-97 Danish Biological Society, board member

92-93 Maternity leave

PUBLICATIONS - last 10 years

Frandsen, G., Muller-Uri, F., Nielsen, M., Mundy, J., and Skriver, K. (1996) Novel plant Ca⁺⁺-binding protein expressed in response to abscisic acid and osmotic stress. J. Biol. Chem. 271, 343-348. 

Skriver, K., Hansen, B.V., and Andersen, M.D. (1996) Functional role of Glu89 in 26 kDa barley endochitinase in relation to the hydrolytic mechanism of plant chitinases. In Chitin Enzymology 2, pp. 103-108, (Muzzarelli, R.A.A., eds.), Atec Edizioni - Grottammare.

Andersen, M.D., Jensen, A., Robertus, J.D., Leah, R., and Skriver, K. (1997) Heterologous expression and characterization of wild-type and mutant forms of a 26 kDa endochitinase from Hordeum vulgare L. Biochem. J. 322, 815-822.

Skriver, K., Schlein, M., Raventos, D, and Mundy, J. (1997) Plantevækst, gener og bioteknologi. Naturens Verden 3, 96-104.

Raventos, D., Skriver, K., Schlein, M., Karnahl, Rogers, J.C., and Mundy, J. (1998) HTR, a Novel Zinc Finger, transcriptional Repressor from Barley. J. Biol. Chem. 273, 23312-23320.

Jensen, R.B., Jensen, K.L., Jespersen, H.M., and Skriver, K. (1998) Widespread occurrence of a highly conserved RING-H2 zinc finger motif in the model plant Arabidopsis thaliana. FEBS Lett. 436, 277-282.

Jensen, R.B., Skriver, K., and Jespersen, H.M. (1999) FZF, a putative, multiple C2H2 zinc finger protein from Arabidopsis thaliana. Plant Mol. Biol. 39, 637. 

Jensen, R.B., Skriver, K., and Jespersen, H.M. PMZ, a cDNA form Arabidopsis thaliana encoding a putative, novel zinc finger motif with homologs in vertebrates and mammals. Plant Mol. Biol. 40, 745. 

Jensen, R.B., Lykke-Andersen, K., Frandsen, G.I., Nielsen, H.B., Haseloff, J., Jespersen, H.M., Mundy, J., and Skriver, K. (2000) Promiscuous and specific phospholipid binding by domains in ZAC, a membrane-associated Arabidopsis protein with an hARF GAP zinc finger and a C2 domain. Plant Mol. Biol. 44, 799-814.

Skriver, K. (2000) In Proteiner, pp. 31-38, (Kielberg, V. and Rasmussen, L., eds.), GAD, Copenhagen.

Jensen, R.B., la Cour, T., Albrethsen, J., Nielsen, M., and Skriver, K. (2001) FYVE zinc finger proteins in the plant model Arabidopsis thaliana: Identification of PtdIns3P-binding residues by comparison of classic and variant FYVE domains. Biochem. J. 359, 165-173.

Olsen, A.N., Mundy, J., and Skriver, K. (2003) Peptomics, identification of novel Arabidopsis peptides with conserved sequence motifs. In Silico Biol. 2, 441-451.

Greve, K., La Cour, T., Jensen, M.K., Poulsen, F.M., and Skriver K. (2003) Interactions between plant RING-H2 and plant-specific NAC (NAM/ATAF1/2/CUC2) proteins: RING-H2 molecular specificity and cellular localization. Biochem. J. 371, 97-108.

Olsen, A.N. and Skriver, K. (2003) Ligand mimicry? Plant-parasitic nematode polypeptide with similarity to CLAVATA3. Trends Plant Sci. 8, 55-57.

la Cour, T., Gupta, R., Rapacki, K., Skriver, K., Poulsen, F.M., and Brunak, S. (2003) NESbase version 1.0: a database of nuclear export signals. Nucleic Acids Res. 31, 393-396.

Olsen, A. N., Ernst, H. A., Lo Leggio, L., Johansson, E., Larsen, S., and Skriver, K. (2004) Preliminary crystallographic analysis of the NAC domain of ANAC, a member of the plant-specific NAC transcription factor family. Acta Crystallogr. D: Biol. Crystallogr. 60, 112-115.

Enst, H. A., Olsen, A. N., Skriver, K., Larsen, S., and Lo Leggio, L. (2004) Structure of the conserved domain of ANAC, a member of the NAC family of plant specific transcription factors. EMBO Rep. 5, 297-303.

Andersen, P., Kragelund, B.B., Olsen, A.N., Larsen, F.H., Poulsen, F.M., and Skriver, K. (2004) Structure and Function of a Prototypical Arabidopsis U-box domain J. Biol. Chem. 279, 40053-40061.

La Cour, T., Kiemer, L., Mølgaard, A., Gupta, R., Skriver, K., and Brunak, S. (2004) Analysis and prediction of leucine-rich nuclear export signals. Protein Eng. Des. Sel. 17, 527-536.

Olsen, A.N., Ernst, H., Lo Leggio, L., and Skriver, K. (2005) NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci. 10, 79-87.

Olsen, A.N., Ernst, H., Lo Leggio, L., and Skriver, K. (2005) DNA-binding specificity and molecular functions of NAC transcription factors. Plant Sci. 169, 785-797.

Ohnishi, T., Juffer, A., Tamoi, M., Skriver, K., and Fukamizo, T. (2005) Barley class II chitinase: an interaction of ionisable side chains essential for catalysis. J. Biochem. 138, 553-562.

Karen Skriver (2005) i Proteiner – oprensning og karakterisering, side 59-65 (Kielberg, V. and Rasmussen, L., red.), Gyldendal, København.

Nielsen, M., Albrethsen, J., Larsen, F.H., and Skriver, K. (2006) The Arabidopsis ADP-

ribosylation factor (ARF) and ARF-like (ARL) system and its regulation by BIG2, a large

ARF-GEF Plant Sci.171, 707-717.

MASTERS/BACHELOR PROJECTS

1) Transcription factors:

Projects focus on defining and characterizing transcriptional activation domains using bioinformatics, protein chemistry, molecular biology, and biophysics. In addition, NAC transcription factor networks are identified using transgenic and proteomics techniques.

2) E3 ubiquitin ligases, function and interactions:

Projects focus on structure and function aspects of U-box E3 ubiquitin ligases involved in regulated protein degradation and use biochemical, bioinformatic, and biophysical approaches. The studies also involve identification of U-box interaction partners using two-hybrid assays and proteomics tools.