What Alphafold tells us about cohesin's retention and release from chromosomes

Abstract

Cohesin is a trimeric complex containing a pair of SMC proteins (Smc1 and Smc3) whose ATPase domains at the end of long coiled coils (CC) are interconnected by Scc1. During interphase, it organizes chromosomal DNA topology by extruding loops in a manner dependent on Scc1s association with two large hook shaped proteins called SA (yeast: Scc3) and Nipbl (Scc2). The latters replacement by Pds5 recruits Wapl, which induces release from chromatin via a process requiring dissociation of Scc1s N-terminal domain (NTD) from Smc3. If blocked by Esco (Eco)-mediated Smc3 acetylation, cohesin containing Pds5 merely maintains pre-existing loops, but a third fate occurs during DNA replication, when Pds5-containing cohesin associates with Sororin and forms structures that hold sister DNAs together. How Wapl induces and Sororin blocks release has hitherto remained mysterious. In the twenty years since their discovery, not a single testable hypothesis has been proposed as to their role. Here, AlphaFold 2 (AF) three-dimensional protein structure predictions lead us to propose formation of a quarternary complex between Wapl, SA, Pds5, and Scc1s NTD, in which the latter is juxtaposed with (and subsequently sequestered by) a highly conserved cleft within Wapls C-terminal domain (CTD). AF also reveals how Scc1s dissociation from Smc3 arises from a distortion of Smc3s CC induced by engagement of SMC ATPase domains, how Esco acetyl transferases are recruited to Smc3 by Pds5, and how Sororin prevents release by binding to the Smc3/Scc1 interface. Our hypotheses explain the phenotypes of numerous existing mutations and are highly testable.