Studies of transcription factor domains and their interactions with other transcription factors

The studies in this thesis deal with different questions concerning interactions of functional domains of factors involved in transcriptional regulation. The first study of this thesis is focused on the target factor binding mechanism of transcriptional activators. Many activators in evolutionary distant species are classified as acidic based on a high content of acidic residues in the activation domain and intrinsically unstructured in solution. Our results indicate that such activation domains interact with target factors through coupled binding and folding of the activation domain after an initial ionic interaction, and demonstrate the generality of this binding mechanism. We propose that target interaction through coupled binding and folding of the recruiting domain is important for the role of activators as regulators of transcription.

In the following study we show that deletion of two regions that mediate interaction with activators in vitro prevents promoter recruitment of the SWI/SNF chromatinremodeling complex in vivo, and causes strongly reduced transcriptional activity of the corresponding genes. This study validates direct interaction between the Swi1- and Snf5 activator binding domains of the S. cerevisiae SWI/SNF complex and activators previously demonstrated in vitro, and importantly indicates that the activator binding domains are essential for the ability of SWI/SNF to function as co-activator.

In the last study we investigate which domains are involved in distinct in vivo function of the paralogous co-repressors Tup11 and Tup12 of the Ssn6/Tup complex in S. pombe. Tup11 and Tup12 have been shown to differ in importance in context of a common complex for subsets of Ssn6/Tup target genes, and it was proposed that this might depend on divergence in the histone-interaction domain. Here we show that distinct in vivo roles of Tup12 do not depend on differences in the highly diverged histoneinteraction domain, but mainly on differences in the overall highly conserved WD40 repeat domain, which putatively mediates interaction with repressors and target factors such as histone modifying complexes and components of the transcriptional machinery.

We propose that clusters of amino acids, putatively located in blade 3 of the WD40 repeat domain, could be important for interaction with distinct target factors of Tup11 and Tup12. Furthermore, we show that the stoichiometry of the Ssn6/Tup complex is likely to change under CaCl2 stress, by a mechanism involving changes in the relative cellular levels of the complex components.

List of scientific papers

I. Ferreira ME, Hermann S, Prochasson P, Workman JL, Berndt KD, Wright AP (2005). Mechanism of transcription factor recruitment by acidic activators. J Biol Chem. 280(23): 21779-84. Epub 2005 Apr 11
https://pubmed.ncbi.nlm.nih.gov/15826952

II. Ferreira ME, Prochasson P, Berndt KD, Workman JL, Wright AP (2009). Activator-binding domains of the SWI/SNF chromatin remodelling complex characterized in vitro are required for its recruitment to promoters in vivo. FEBS J. 276(9): 2557-2565. [Epub 2009 Mar 18]

III. Ferreira ME, Nilsson J, Berndt KD, Wright AP (2009). Protein domains underlying functional divergence between the Tup11 and Tup12 co-repressor proteins in fission yeast. [Manuscript]