RNA-controlled polymorphism in the in vivo assembly of 180-subunit and 120-subunit virions from a single capsid protein

Repeated, specific interactions between capsid protein (CP) subunits direct virus capsid assembly and exemplify regulated protein-protein interactions . The results presented here reveal a striking in vivo switch in CP assembl y. Using cryoelectron microscopy, three-dimensional image reconstruction, a nd molecular modeling, we show that brome mosaic virus (BMV) CP can assembl e in vivo two remarkably distinct capsids that selectively package BMV-deri ved RNAs in the absence of BMV RNA replication: a 180-subunit capsid indist inguishable from virions produced in natural infections and a previously un observed BMV capsid type with 120 subunits arranged as 60 CP dimers. Each s uch dimer contains two CPs in distinct, nonequivalent environments, in cont rast to the quasi-equivalent CP environments throughout the 180-subunit cap sid. This 120-subunit capsid utilizes most of the CP interactions of the 18 0-subunit capsid plus nonequivalent CP-CP interactions. Thus, the CP of BMV , and perhaps other viruses, can encode CP-CP interactions that are not app arent from mature virions and may function in assembly or disassembly. Shar ed structural features suggest that the 120- and 120-subunit capsids share assembly steps and that a common pentamer of CP dimers may be an important assembly intermediate. The ability of a single CP to switch between distinc t capsids by means of alternate interactions also implies reduced evolution ary barriers between different capsid structures. The in vivo switch betwee n alternate BMV capsids is controlled by the RNA packaged: a natural BMV ge nomic RNA was packaged in 180-subunit capsids, whereas an engineered mRNA c ontaining only the BMV CP gene was packaged in 120-subunit capsids. RNA fea tures can thus direct the assembly of a ribonucleoprotein complex between a lternate structural pathways.