Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization

Abstract

Under stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In , dimerization of 70S ribosomes into 100S requires the action of the ribosome modulation factor (RMF) and the hibernation-promoting factor (HPF). Most other bacteria lack RMF and instead contain a long form HPF (LHPF), which is necessary and sufficient for 100S formation. While some structural information exists as to how RMF and HPF mediate formation of 100S (100S), structural insight into 100S formation by LHPF has so far been lacking. Here we present a cryo-EM structure of the hibernating 100S (100S), revealing that the C-terminal domain (CTD) of the LHPF occupies a site on the 30S platform distinct from RMF Moreover, unlike RMF, the HPF-CTD is directly involved in forming the dimer interface, thereby illustrating the divergent mechanisms by which 100S formation is mediated in the majority of bacteria that contain LHPF, compared to some γ-proteobacteria, such as.

RNA polymerase I activation and hibernation: unique mechanisms for unique genes

“…Pol I hibernation might protect the enzyme from degradation and, at the same time, allow fast reactivation when favourable growth conditions are restored. Interestingly, a similar mode of hibernation by dimerization has been observed for bacterial ribosomes [34,35]. Nevertheless, while the formation of ribosome homodimers, also termed disomes, relies on external factors that bind prior to dimerization, structural studies established that Pol I dimerization does not require binding of external factors [19,20].…”

Disassembly of theStaphylococcus aureushibernating 100S ribosome by an evolutionarily conserved GTPase

“…Furthermore, the parallel beta-sheet interactions between the two 70S ribosomes are not rigid (19), and disrupting the flexible loop linking the CTD and NTD impairs dimerization (18). These findings suggest that the dissociation of 100S ribosome involves an active mechanism to dislodge the dimerizing factors from the ribosome.…”

“…During HPF-induced dimerization, a 30S head rotation of the S. aureus 100S ribosome stabilizes the dimerization interface consisting of the rRNA h26, and h40 and the ribosomal protein uS2 (19). This 30S swiveling was not observed in the B. subtilis 30S-70S subcomplex (18).…”

“…These studies lead to a model whereby the formation of the 100S complex sequesters the ribosome pool away from active translation, and 70S self-dimerization prevents ribosome degradation by an unknown pathway (3,17). During the stationary phase, the 100S ribosomes are presumably dissociated and reused for new cycles of translation, thereby maintaining cell viability (1,3,16,18). The process and dissociation factors involved in the reversible transition of silent 100S to a translationally competent 70S ribosome remain poorly understood.…”

“…1). In addition, the N-terminal domain (NTD) of HPF inhibits translation by sterically occluding the mRNA and the anticodon tRNA binding sites (18)(19)(20). During HPF-induced dimerization, a 30S head rotation of the S. aureus 100S ribosome stabilizes the dimerization interface consisting of the rRNA h26, and h40 and the ribosomal protein uS2 (19).…”