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This Sandbox is Reserved from 06/12/2018, through 30/06/2019 for use in the course "Structural Biology" taught by Bruno Kieffer at the University of Strasbourg, ESBS. This reservation includes Sandbox Reserved 1480 through Sandbox Reserved 1543.

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2RO1 (KAP-1)2RO1 (KAP-1)

KAP-1 (KRAB – associated protein 1) is a protein of the KRAB protein family (Krüppel-associated box). These KRAB domain is a domain of repression which is encoded by many zinc finger protein-based transcription factors (KRAB zinc finger proteins or KRAP-ZFPs proteins).[1]

KAP-1 is also known as Tripartite motif-containing 28 (TRIM28) and as transcriptional intermediary factor 1β (TIF1β). Indeed, KAP-1 is one of the TRIM proteins (wich code for TRIM genes). Among these TRIM proteins, there is the TIF1 family proteins, of which is part KAP-1 (that’s why KAP-1 is also known as TIF1β and TRIM28).[2]

KAP-1 is localized in the nucleus and interacts whith specific regions of the chromatin. This protein plays role in many phenomena as the regulation of transcription, the cellular differenciation and proliferation or even the reparation of DNA damages. Sumoylation can activate the protein in many of its mechanisms while phosphorylation can deactivate the protein. [3]

Structure As all the TIF1 proteins, KAP-1 owns a N-terminal tripartite motif (TRIM). This motif is a protein-protein interface which contains an RBCC domain (itself composed of a Ring finger, two B-box zinc fingers, and a coiled-coil domain) and a central TIF1 signature sequence (TSS).[3] KAP-1 has a C-terminal motif composed of one homeodomain (PHD) and one bromodomain. Moreover, KAP-1 possesses a central binding domain called HP1 (for heterochromatin protein 1). As said before, the fisrt part of KAP-1 is the N-Terminal motif, within we can find the RBCC sequence. The RBCC domain has a high affinity for protein interactions. Thus, this is the RBCC domain which alllows the interaction between KAP-1 and the 3 -ends of ZNF genes of KRAB-ZNFs domains. In this way, KAP-1 binds as a homotrimer to a single KRAB domain. There is then an oligomerization which provides folding of the KRAB domain to encapsulates it in a protease-resistant core. RBCC is composed of three subdomains. One of these is the ring subdomain. This is a double zinc-binding C3HC4 motif. The second subdomain is composed of the two B-box which are cysteine-rich zinc-binding motif of the form CHC3H2. These latter interacts with the last subdomain : the coiled-coil domain. These two subdomains form an extended hydrophobic helical region. It’s here that protein-protein interactions take place. Next to the RBCC motif, there is the TSS sequence which is tryptophan and phenylalanine rich. We know that the deletion of this sequence cancel the transcriptional repression mediated by TIF1γ. [4] Between the N-Terminal and the C-Terminal motif, KAP-1 owns a HP1 binding domain which is a hydrophobic PxVxL pentapeptide. This pentapeptide allows the interaction of KAP-1 with the chromoshadow domain of all the proteins of the HP1 family. This is necessary for the repression of reporter genes. This domain is proline, glycine and serine rich. [4] Finally, the last part of KAP-1, which is the C-terminal motif, is the tandem formed by the PHD and the bromodomain (or PB domain). These two motifs are both very important and are closely associated to play a role in the transcriptional repression.[4] Function KAP-1 has many differents functions and some of them have yet to be studied. KAP-1 is involved in the regulation of transcription, the reparation of DNA damage but also in the cellular differenciation and proliferation and in the apoptosis. [4] Regulation of transcription KAP-1 acts as a transcriptional corepressor for KRAB-ZFP proteins (KRAB domain-containing zinc finger proteins), which are proteins containing a KRAB domain. Indeed, KAP-1 make the link between the KRAB domain of KRAB-ZFPs and the transcriptional repression machinery. Because KAP-1 is not able to bind directly the DNA, it has to do a protein-protein interaction. This interaction takes place in the TRIM sequence. KAP-1 can thus coordinate and recruit to the promoter regions of KRAB target genes several components of gene silencing machinery, like the histone deacetylase complex NuRD or the histone methyltransferase SETDB1 (which specifically methylates histone H3 at Lys-9 (H3K9me). In this way, KAP-1 is able to change the form of the chromatin and to do histones modifications at target sites, particurlay by using sumoylation. Indeed, it has recently been reported that sumoylation, a post translationnal modification which affects lysines, influences the function of KAP-1 as transcriptional co-repressor. [5] The lysine sumoylation can change the conformation and thus the function of a protein and its interactions with others molecules. In this way, sumoylation of KAP-1 can impact the transcriptional control that it made. The sumoylation of KAP-1 recruit the SETDB1 histone methyltransferase and the NuRD remodeling complex by binding sumo proteins to interacting sequences. This binding leads to the remodeling of chromatin and modify the target gene. This phenomenon occurs within the tandem PHD-bromodomain but the recognition of the KRAB domain occurs in the RBCC sequence. [2] The strongest KAP-1 binding site is the 3-ends of ZNF genes (of course present in all KRAB-ZFPs proteins) but recent ChIP-seq experiments have identified thousands of KAP1-binding sites. [4] DNA damage repair response KAP-1 also plays a role in the repair of DNA when it is damaged. These damages are cytotoxic DNA lesions and can be for example double-strand breaks (DSB). These damages requires the action of the nuclear protein kinase ATM. For example, when the DNA is damaged by DSB, ATM allows the relaxation of the chromatin to allow to the DNA repair proteins to do their job. The effector of this interaction is precisely KAP-1. Indeed, in response to DSB, KAP-1 is phosphorylated thanks to the ATM on the Serine 824. In this way, without KAP-1, there is no more relaxation of the chromatin and the cell become hypersensitive to DSB-inducing agents. [6] The hypothesis is thus that the phosphorylation of KAP-1 results in the loss of sumoylated KAP-1 form, which is the activated form of KAP-1. That can lead to the derepression of the target genes of KAP-1. In this way, we can say that it exists an equilibrium between the phosphorylated and the sumoylated forms of KAP-1, which influences its function of repression. [4] Importance of the tandem PHD-Bromodomain Kap-1 structure have a tandem PHD finger- bromodomain. This tandem is implicate in the repression of specific gene. The tandem is formed with the first helix, of an atypical bromodomain which forms a central hydrophobic core. Hence, three helix of the bromodomain and the zinc binding PHD finger are anchored in the central core. The bromodomain adopt four helix bundle (100 amino-acid) and the PHD finger contain an antiparallel sheet Béta (60 amino-acid).[2] Sumoylated Kap-1 is the highly repressive form. That’s why the adjacent KAP-1 bromodomain is sumoylated by the PHD which functioning as an intramolecular E3 ligase. The bromodomain need to be sumoylate because it allows interaction with SETDB1 (SET domain, bifurcated 1) in order to stimule it H3K9me3 specific histone methyltransferase activity. The bromodomain can also interact with Mi2 which is an isoform of the Mi2 protein found in NuRD complex.[4] Therapeutical perspective KAP-1 can represent a good perspective for some therapies because it is implicate in the etablishment of viral latency, for example in the replication of Epstein-Barr Virus (EBV), Kaposi's sarcoma-associated herpes virus (KSHV), Human cytomegalovirus (HCMV) and for endogenous retroviruses. [7][8]Indeed, during the lytic infection, KAP-1 binds the viral genome and plays his role of repressor for the transcription of this genome (KAP-1 is activated when it is sumoylated and inactivate when it is phosphorylated). In this way, when KAP-1 is phosphorylated on serine 824 (by mTOR or ATM for example), it is not anymore able to recruit SETDB1 which is necessary to regulate the transcription. KAP-1 become thus inactive and the latency exits, and the viral genome will be transcribed and replicate. The result is so the switch from viral latency to the lytic cycle. The idea is then to use this characteristic of KAP-1 to develop a potential therapy able to purge the virus from infected individuals.[7][8][9]

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ReferencesReferences

[1] Eishou Matsuda, Yasutoshi Agata, Manabu Sugai, Tomoya Katakai, Hiroyuki Gonda, and Akira Shimizu, Targeting of Krüppel-associated Box-containing Zinc Finger Proteins to Centromeric Heterochromatin, IMPLICATION FOR THE GENE SILENCING MECHANISMS, Received for publication, November 27, 2000, and in revised form, January 18, 2001 Published, JBC Papers in Press, January 19, 2001.

[2] Lei Zeng, Kyoko L Yap, Alexey V Ivanov, Xueqi Wang, Shiraz Mujtaba, Olga Plotnikova, Frank J Rauscher III, and Ming-Ming Zhou, Structural insights into human KAP1 PHD finger–bromodomain and its role in gene silencing, Published in final edited form as:Nat Struct Mol Biol. 2008 June ; 15(6): 626–633.

[3] J R Friedman, W J Fredericks, D E Jensen, et al., KAP-1, a novel corepressor for the highly conserved KRAB repression domain, Genes Dev. 1996 10: 2067-2078.

[4] Sushma Iyengar and Peggy J. Farnham, KAP1 Protein: An Enigmatic Master Regulator of the Genome, Published, JBC Papers in Press, June 7, 2011,

[5] Xu Li, Yung-Kang Lee, Jen-Chong Jeng, Yun Yen, David C. Schultz , Hsiu-Ming Shih, and David K. Ann, Role for KAP1 Serine 824 Phosphorylation and Sumoylation/Desumoylation Switch in Regulating KAP1-mediated Transcriptional Repression, Received for publication, August 20, 2007, and in revised form, October 9, 2007 Published, JBC Papers in Press, October 17, 2007.

[6] Yael Ziv, Dana Bielopolski, Yaron Galanty, Claudia Lukas, Yoichi Taya, David C. Schultz, Jiri Lukas, Simon Bekker-Jensen, Jiri Bartek and Yosef Shiloh, Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM- and KAP-1 dependent pathway, Received 22 March 2006; accepted 4 July 2006; published online 23 July 2006.

[7] Benjamin Rauwel, Suk Min Jang, Marco Cassano, Adamandia Kapopoulou, Isabelle Barde, Didier Trono , Release of human cytomegalovirus from latency by a KAP1/TRIM28 phosphorylation switch, Elife, April 7, 2015.

[8] Helen M. Rowe, Johan Jakobsson, Daniel Mesnard, Jacques Rougemont, Séverine Reynard, Tugce Aktas, Pierre V. Maillard, Hillary Layard-Liesching, Sonia Verp, Julien Marquis, François Spitz, Daniel B. Constam & Didier Trono, KAP1 controls endogenous retroviruses in embryonic stem cells, Nature, January 14, 2010.

[9] Andreia Lee, Oya Cingöz, Yosef Sabo, Stephen P. Goff, Characterization of interaction between Trim28 and YY1 in silencing proviral DNA of Moloney murine leukemia virus, Received for publication, August 20, 2017, Revised 10 January 2018, Accepted 12 January 2018, Published, Virology , February 23, 2018.