Date Published: October 11, 2018
Publisher: Public Library of Science
Author(s): Sankaran Sandhya, Aditi Maulik, Malyasree Giri, Mahavir Singh, Wenqing Xu.
BAF250a and BAF250b are subunits of the SWI/SNF chromatin-remodeling complex that recruit the complex to chromatin allowing transcriptional activation of several genes. Despite being the central subunits of the SWI/SNF complex, the structural and functional annotation of BAF250a/b remains poorly understood. BAF250a (nearly 2200 residues protein) harbors an N-terminal DNA binding ARID (~110 residues) and a C-terminal folded region (~250 residues) of unknown structure and function, recently annotated as BAF250_C. Using hydrophobic core analysis, fold prediction and comparative modeling, here we have defined a domain boundary and associate a β-catenin like ARM-repeat fold to the C-terminus of BAF250a that encompass BAF250_C. The N-terminal DNA-binding ARID is found in diverse domain combinations in proteins imparting unique functions. We used a comparative sequence analysis based approach to study the ARIDs from diverse domain contexts and identified conserved residue positions that are important to preserve its core structure. Supporting this, mutation of one such conserved residue valine, at position 1067, to glycine, resulted in destabilization, loss of structural integrity and DNA binding affinity of ARID. Additionally, we identified a set of conserved and surface-exposed residues unique to the ARID when it co-occurs with the ARM repeat containing BAF250_C in BAF250a. Several of these residues are found mutated in somatic cancers. We predict that these residues in BAF250a may play important roles in mediating protein-DNA and protein-protein interactions in the BAF complex.
Chromatin remodeling complexes are specialized cellular machinery consisting of a number of proteins that work in concert, to remodel the nucleosome (histone-DNA complex) structure during various cellular processes such as transcription, replication, and repair leading to regulation of gene expression . Both the histone modification enzymes and the ATP-dependent complexes play key roles in mediating this reorganization. While the former modify histones, the latter utilize ATP hydrolysis to drive the local disruption or alter association of histones with DNA. Such complexes, as observed in humans, yeast and drosophila typically involve as many as twelve to fifteen proteins [2,3]. Each protein is known to exist in more than one isoform, thus expanding the scope for the formation of a wide range of complexes that can function distinctly from each other. Indeed, it is suggested that the controlled expression of specific sub-units in various developmental stages is possibly a means to regulate the composition of individual complexes and their interactions with intended targets [4,5].
Using hydrophobic core analysis based SEG-HCA approach, here we report several regions in BAF250a that harbor functionally important motifs, which are likely to be folded with a hydrophobic core. The predicted regions included the DNA binding ARID and a β-catenin like ARM-repeat fold containing BAF250_C domains. Using rigorous sequence and phylogenetic analysis, we showed that ARM-repeat fold in association with ARID is only found in BAF250a homologues (in ARCH2) suggesting that these two domains co-evolved in these proteins. While instances of the ARM repeat domains interacting with proteins that harbor a DNA-binding domain are known, their co-occurrence in a single protein is reported here for the first time [58,59]. We believe that these two domains co-occur to facilitate the interactions of the ARID containing proteins with other members of the SWI/SNF complex. Alignment of all ARID sequences (across all domain architectures) resulted in identification of a set of conserved residue positions that are critical for the maintenance of ARID fold. In a previous study a hydrophobic cluster was identified that consisted of conserved residues V1058, I1061, V1067, L1076, Y1096, and K1093. Here, we provide an experimental validation that mutation of a conserved residue (V1067G) results in gross destabilization of ARID fold that impairs its DNA binding functions. Using ITC experiments we showed that V1067G mutation leads to a drastic decrease (~10 fold) in the DNA binding affinity of ARID.