Structural insights into the novel ARM-repeat protein CTNNBL1 and its association with the hPrp19-CDC5L complex

Disease-associated CTNNBL1 mutation impairs somatic hypermutation by decreasing nuclear AID

Patients with common variable immunodeficiency associated with autoimmune cytopenia (CVID+AIC) generate few isotype-switched B cells with severely decreased frequencies of somatic hypermutations (SHMs), but their underlying molecular defects remain poorly characterized. We identified a CVID+AIC patient who displays a rare homozygous missense M466V mutation in β-catenin-like protein 1 (CTNNBL1). Because CTNNBL1 binds activation-induced cytidine deaminase (AID) that catalyzes SHM, we tested AID interactions with the CTNNBL1 M466V variant. We found that the M466V mutation interfered with the association of CTNNBL1 with AID, resulting in decreased AID in the nuclei of patient EBV-transformed B cell lines and of CTNNBL1 466V/V Ramos B cells engineered to express only CTNNBL1 M466V using CRISPR/Cas9 technology. As a consequence, the scarce IgG+ memory B cells from the CTNNBL1 466V/V patient showed a low SHM frequency that averaged 6.7 mutations compared with about 18 mutations per clone in healthy-donor counterparts. In addition, CTNNBL1 466V/V Ramos B cells displayed a decreased incidence of SHM that was reduced by half compared with parental WT Ramos B cells, demonstrating that the CTNNBL1 M466V mutation is responsible for defective SHM induction. We conclude that CTNNBL1 plays an important role in regulating AID-dependent antibody diversification in humans.

Small angle X-ray scattering studies of CTNNBL1 dimerization and CTNNBL1/CDC5L complex

The hPrp19/CDC5L complex is a non-snRNP spliceosome complex that plays a key role in the spliceosome activation during pre-mRNA splicing, and CTNNBL1 and CDC5L are essential components of the complex. In this study, to investigate the oligomeric state of CTNNBL1 in solution, we performed small angle X-ray scattering experiments in various concentrations of NaCl. We observed that CTNNBL1 existed as a dimer in physiological NaCl concentrations. Site-directed mutagenesis experiment of CTNNBL1 confirmed that N-terminal capping region and the first four ARM repeats are important for dimerization of the protein. We also found that the positively-charged NLS3-containing region (residues 197-235) of CDC5L bound to the negatively-charged patch of CTNNBL1 and that the CTNNBL1/CDC5L complex formed a heterotetramer consisting of one CTNNBL1 dimer and one CDC5L dimer. Moreover, reconstruction of 3D models of CTNNBL1/CDC5L complexes containing CTNNBL1 and three different truncated forms of CDC5L showed that the CDC5L(141-196) region and the CDC5L(236-377) region were positioned at the top of the N-terminal capping region and at the bottom of ARM VII of CTNNBL1, respectively.

CTNNBL1 facilitates the association of CWC15 with CDC5L and is required to maintain the abundance of the Prp19 spliceosomal complex

In order to catalyse the splicing of messenger RNA, multiple proteins and RNA components associate and dissociate in a dynamic highly choreographed process. The Prp19 complex is a conserved essential part of the splicing machinery thought to facilitate the conformational changes the spliceosome undergoes during catalysis. Dynamic protein interactions often involve highly disordered regions that are difficult to study by structural methods. Using amine crosslinking and hydrogen-deuterium exchange coupled to mass spectrometry, we describe the architecture of the Prp19 sub-complex that contains CTNNBL1. Deficiency in CTNNBL1 leads to delayed initiation of cell division and embryonic lethality. Here we show that in vitro CTNNBL1 enhances the association of CWC15 and CDC5L, both core Prp19 complex proteins and identify an overlap in the region of CDC5L that binds either CTNNBL1 or CWC15 suggesting the two proteins might exchange places in the complex. Furthermore, in vivo, CTNNBL1 is required to maintain normal levels of the Prp19 complex and to facilitate the interaction of CWC15 with CDC5L. Our results identify a chaperone function for CTNNBL1 within the essential Prp19 complex, a function required to maintain the integrity of the complex and to support efficient splicing.