posted on 2024-03-22, 14:41authored byFrancesco Guidarelli Mattioli, Andrea Saltalamacchia, Alessandra Magistrato
RNA ATPases/helicases remodel substrate RNA–protein
complexes
in distinct ways. The different RNA ATPases/helicases, taking part
in the spliceosome complex, reshape the RNA/RNA-protein contacts to
enable premature-mRNA splicing. Among them, the bad response to refrigeration
2 (Brr2) helicase promotes U4/U6 small nuclear (sn)RNA unwinding via
ATP-driven translocation of the U4 snRNA strand, thus playing a pivotal
role during the activation, catalytic, and disassembly phases of splicing.
The plastic Brr2 architecture consists of an enzymatically active
N-terminal cassette (N-cassette) and a structurally similar but inactive
C-terminal cassette (C-cassette). The C-cassette, along with other
allosteric effectors and regulators, tightly and timely controls Brr2’s
function via an elusive mechanism. Here, microsecond-long molecular
dynamics simulations, dynamical network theory, and community network
analysis are combined to elucidate how allosteric effectors/regulators
modulate the Brr2 function. We unexpectedly reveal that U4 snRNA itself
acts as an allosteric regulator, amplifying the cross-talk of distal
Brr2 domains and triggering a conformational reorganization of the
protein. Our findings offer fundamental understanding into Brr2’s
mechanism of action and broaden our knowledge on the sophisticated
regulatory mechanisms by which spliceosome ATPases/helicases control
gene expression. This includes their allosteric regulation exerted
by client RNA strands, a mechanism that may be broadly applicable
to other RNA-dependent ATPases/helicases.