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  • 1.
    Ferreira, Monica E.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska institutet.
    Studies of transcription factor domains and their interactions with other transcription factors2009Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    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.

  • 2.
    Ferreira, Monica E.
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Berndt, Kurt D.
    Södertörns högskola, Institutionen för livsvetenskaper, Kemi.
    Nilsson, Johan
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Wright, Anthony P. H.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    WD40 Domain Divergence Is Important for Functional Differences between he Fission Yeast Tup11 and Tup12 Co-Repressor Proteins2010Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 5, nr 6, artikkel-id e11009Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have previously demonstrated that subsets of Ssn6/Tup target genes ave distinct requirements for the Schizosaccharomyces pombe homologs of he Tup1/Groucho/TLE co-repressor proteins, Tup11 and Tup12. The very igh level of divergence in the histone interacting repression domains f the two proteins suggested that determinants distinguishing Tup11 and up12 might be located in this domain. Here we have combined hylogenetic and structural analysis as well as phenotypic haracterization, under stress conditions that specifically require up12, to identify and characterize the domains involved in up12-specific action. The results indicate that divergence in the epression domain is not generally relevant for Tup12-specific function. nstead, we show that the more highly conserved C-terminal WD40 repeat omain of Tup12 is important for Tup12-specific function. Surface amino cid residues specific for the WD40 repeat domain of Tup12 proteins in ifferent fission yeasts are clustered in blade 3 of the propeller-like tructure that is characteristic of WD40 repeat domains. The Tup11 and up12 proteins in fission yeasts thus provide an excellent model system or studying the functional divergence of WD40 repeat domains.

  • 3.
    Ferreira, Monica E
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Hermann, Stefan
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Prochasson, P
    Stowers Institute for Medical Research, Kansas City, USA.
    Workman, J L
    Stowers Institute for Medical Research, Kansas City, USA.
    Berndt, Kurt D
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Wright, Athony P H
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Mechanism of transcription factor recruitment by acidic activators2005Inngår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 280, nr 23, s. 21779-21784Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Many transcriptional activators are intrinsically unstructured yet display unique, defined conformations when bound to target proteins. Target-induced folding provides a mechanism by which activators could form specific interactions with an array of structurally unrelated target proteins. Evidence for such a binding mechanism has been reported previously in the context of the interaction between the cancer-related c-Myc protein and the TATA-binding protein, which can be modeled as a two-step process in which a rapidly forming, low affinity complex slowly converts to a more stable form, consistent with a coupled binding and folding reaction. To test the generality of the target-induced folding model, we investigated the binding of two widely studied acidic activators, Gal4 and VP16, to a set of target proteins, including TATA-binding protein and the Swi1 and Snf5 subunits of the Swi/Snf chromatin remodeling complex. Using surface plasmon resonance, we show that these activator-target combinations also display bi-phasic kinetics suggesting two distinct steps. A fast initial binding phase that is inhibited by high ionic strength is followed by a slow phase that is favored by increased temperature. In all cases, overall affinity increases with temperature and, in most cases, with increased ionic strength. These results are consistent with a general mechanism for recruitment of transcriptional components to promoters by naturally occurring acidic activators, by which the initial contact is mediated predominantly through electrostatic interactions, whereas subsequent target-induced folding of the activator results in a stable complex.

  • 4.
    Ferreira, Monica E.
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Nilsson, Johan
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Berndt, Kurt D.
    Södertörns högskola, Institutionen för livsvetenskaper, Kemi. Karolinska Institutet.
    Wright, Anthony P. H.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Protein domains underlying functional divergence between the Tup11 and Tup12 co-repressor proteins in fission yeastManuskript (preprint) (Annet vitenskapelig)
  • 5.
    Ferreira, Monica E.
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska instiutet.
    Prochasson, Philippe
     Stowers Institute for Medical Research, Kansas City, MO, USA.
    Berndt, Kurt D.
    Södertörns högskola, Institutionen för livsvetenskaper, Kemi. Karolinska institutet.
    Workman, Jerry L.
    Stowers Institute for Medical Research, Kansas City, MO, USA.
    Wright, Anthony P. H.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska institutet.
    Activator-binding domains of the SWI/SNF chromatin remodeling complex characterized in vitro are required for its recruitment to promoters in vivo2009Inngår i: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 276, nr 9, s. 2557-2565Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Interaction between acidic activation domains and the activator-binding domains of Swi1 and Snf5 of the yeast SWI/SNF chromatin remodeling complex has previously been characterized in vitro. Although deletion of both activator-binding domains leads to phenotypes that differ from the wild-type, their relative importance for SWI/SNF recruitment to target genes has not been investigated. In the present study, we used chromatin immunoprecipitation assays to investigate the individual and collective importance of the activator-binding domains for SWI/SNF recruitment to genes within the GAL regulon in vivo. We also investigated the consequences of defective SWI/SNF recruitment for target gene activation. We demonstrate that deletion of both activator-binding domains essentially abolishes galactose-induced SWI/SNF recruitment and causes a reduction in transcriptional activation similar in magnitude to that associated with a complete loss of SWI/SNF activity. The activator-binding domains in Swi1 and Snf5 make approximately equal contributions to the recruitment of SWI/SNF to each of the genes studied. The requirement for SWI/SNF recruitment correlates with GAL genes that are highly and rapidly induced by galactose.

  • 6. Rich, Rebecca L.
    et al.
    Papalia, Giuseppe A.
    Flynn, Peter J.
    Furneisen, Jamie
    Quinn, John
    Klein, Joshua S.
    Katsamba, Phini S.
    Waddell, M. Brent
    Scott, Michael
    Thompson, Joshua
    Berlier, Judie
    Corry, Schuyler
    Baltzinger, Mireille
    Zeder-Lutzi, Gabrielle
    Schoenemann, Andreas
    Clabbers, Anca
    Wieckowski, Sebastien
    Murphy, Mary M.
    Page, Phillip
    Ryan, Thomas E.
    Duffner, Jay
    Ganguly, Tanmoy
    Corbin, John
    Gautam, Satyen
    Anderluh, Gregor
    Bavdek, Andrej
    Reichmann, Dana
    Yadav, Satya P.
    Hommema, Eric
    Pol, Ewa
    Drake, Andrew
    Klakamp, Scott
    Chapman, Trevor
    Kernaghan, Dawn
    Miller, Ken
    Schuman, Jason
    Lindquist, Kevin
    Herlihy, Kara
    Murphy, Michael B.
    Bohnsack, Richard
    Andrien, Bruce
    Brandani, Pietro
    Terwey, Danny
    Millican, Rohn
    Darling, Ryan J.
    Wang, Liann
    Carter, Quincy
    Dotzlaf, Joe
    Lopez-Sagaseta, Jacinto
    Campbell, Islay
    Torreri, Paola
    Hoos, Sylviane
    England, Patrick
    Liu, Yang
    Abdiche, Yasmina
    Malashock, Daniel
    Pinkerton, Alanna
    Wong, Melanie
    Lafer, Eileen
    Hinck, Cynthia
    Thompson, Kevin
    Di Primo, Carmelo
    Joyce, Alison
    Brooks, Jonathan
    Torta, Federico
    Hagel, Anne Birgitte Bagge
    Krarup, Janus
    Pass, Jesper
    Ferreira, Monica
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Shikov, Sergei
    Mikolajczyk, Malgorzata
    Abe, Yuki
    Barbato, Gaetano
    Giannetti, Anthony M.
    Krishnamoorthy, Ganeshram
    Beusink, Bianca
    Satpaev, Daulet
    Tsang, Tiffany
    Fang, Eric
    Partridge, James
    Brohawn, Stephen
    Horn, James
    Pritsch, Otto
    Obal, Gonzalo
    Nilapwar, Sanjay
    Busby, Ben
    Gutierrez-Sanchez, Gerardo
    Das Gupta, Ruchira
    Canepa, Sylvie
    Witte, Krista
    Nikolovska-Coleska, Zaneta
    Cho, Yun Hee
    D'Agata, Roberta
    Schlick, Kristian
    Calvert, Rosy
    Munoz, Eva M.
    Hernaiz, Maria Jose
    Bravman, Tsafir
    Dines, Monica
    Yang, Min-Hsiang
    Puskas, Agnes
    Boni, Erica
    Li, Jiejin
    Wear, Martin
    Grinberg, Asya
    Baardsnes, Jason
    Dolezal, Olan
    Gainey, Melicia
    Anderson, Henrik
    Peng, Jinlin
    Lewis, Mark
    Spies, Peter
    Trinh, Quyhn
    Bibikov, Sergei
    Raymond, Jill
    Yousef, Mohammed
    Chandrasekaran, Vidya
    Feng, Yuguo
    Emerick, Anne
    Mundodo, Suparna
    Guimaraes, Rejane
    McGirr, Katy
    Li, Yue-Ji
    Hughes, Heather
    Mantz, Hubert
    Skrabana, Rostislav
    Witmer, Mark
    Ballard, Joshua
    Martin, Loic
    Skladal, Petr
    Korza, George
    Laird-Offringa, Ite
    Lee, Charlene S.
    Khadir, Abdelkrim
    Podlaski, Frank
    Neuner, Phillippe
    Rothacker, Julie
    Rafique, Ashique
    Dankbar, Nico
    Kainz, Peter
    Gedig, Erk
    Vuyisich, Momchilo
    Boozer, Christina
    Ly, Nguyen
    Toews, Mark
    Uren, Aykut
    Kalyuzhniy, Oleksandr
    Lewis, Kenneth
    Chomey, Eugene
    Pak, Brian J.
    Myszka, David G.
    A global benchmark study using affinity-based biosensors2009Inngår i: Analytical Biochemistry, ISSN 0003-2697, E-ISSN 1096-0309, Vol. 386, nr 2, s. 194-216Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To explore the variability in biosensor studies, 150 participants from 20 countries were given the same protein samples and asked to determine kinetic rate constants for the interaction. We chose a protein system that was amenable to analysis using different biosensor platforms as well as by users of different expertise levels. The two proteins (a 50-kDa Fab and a 60-kDa glutathione S-transferase [GST] antigen) form a relatively high-affinity complex, so participants needed to optimize several experimental parameters, including ligand immobilization and regeneration conditions as well as analyte concentrations and injection/dissociation times. Although most participants collected binding responses that could be fit to yield kinetic parameters, the quality of a few data sets could have been improved by optimizing the assay design. Once these outliers were removed, the average reported affinity across the remaining panel of participants was 620 pM with a standard deviation of 980 pM. These results demonstrate that when this biosensor assay was designed and executed appropriately, the reported rate constants were consistent, and independent of which protein was immobilized and which biosensor was used.

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