Stringent response-mediated control of rRNA processing via the ribosomal assembly GTPase Era
P-loop GTPases are widely conserved across all domains of life. These enzymes act as molecular switches, cycling between inactive GDP-bound, and active GTP-bound states. Our previous work identified the Staphylococcus aureus GTPase Era as a binding target for the stringent response alarmone (p)ppGpp. Here we show that, unlike in Escherichia coli, Era is not essential in S. aureus but is important for 30S ribosomal subunit assembly. We employ bacterial two-hybrid and split luciferase approaches to show that Era interacts with the endonuclease YbeY, a protein of unknown function YbeZ, and the DEAD-box RNA helicase CshA in E. coli and natively in S. aureus. We determine that both Era and CshA are cold shock proteins required for virulence and rRNA processing. Era and CshA also form direct interactions with the (p)ppGpp synthetase RSH, an interaction required for controlling (p)ppGpp levels in response to cold shock. Taken together, we conclude that Era acts as an intermediary protein, directing enzymes involved in rRNA maturation to their site of action, an activity which, under stress, is controlled by the stringent response.