title: The stringent factor RelA adopts an open conformation on the ribosome to stimulate ppGpp synthesis.
abstract: Under stress conditions, such as nutrient starvation, deacylated tRNAs bound within the ribosomal A-site are recognized by the stringent factor RelA, which converts ATP and GTP/GDP to (p)ppGpp. The signaling molecules (p)ppGpp globally rewire the cellular transcriptional program and general metabolism, leading to stress adaptation. Despite the additional importance of the stringent response for regulation of bacterial virulence, antibiotic resistance and persistence, structural insight into how the ribosome and deacylated-tRNA stimulate RelA-mediated (p)ppGpp has been lacking. Here, we present a cryo-EM structure of RelA in complex with the Escherichia coli 70S ribosome with an average resolution of 3.7 Å and local resolution of 4 to >10 Å for RelA. The structure reveals that RelA adopts a unique 'open' conformation, where the C-terminal domain (CTD) is intertwined around an A/T-like tRNA within the intersubunit cavity of the ribosome and the N-terminal domain (NTD) extends into the solvent. We propose that the open conformation of RelA on the ribosome relieves the autoinhibitory effect of the CTD on the NTD, thus leading to stimulation of (p)ppGpp synthesis by RelA.
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, Munich 81377, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Arenz
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, Munich 81377, Germany.
authors.forename: Maha
authors.initials: M
authors.lastname: Abdelshahid
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, Munich 81377, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Sohmen
authors.affiliation: University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia.
authors.forename: Roshani
authors.initials: R
authors.lastname: Payoe
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, Munich 81377, Germany.
authors.forename: Agata L
authors.initials: AL
authors.lastname: Starosta
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, Munich 81377, Germany.
authors.forename: Otto
authors.initials: O
authors.lastname: Berninghausen
authors.affiliation: University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, SE-901 87 Umeå, Sweden.
authors.forename: Vasili
authors.initials: V
authors.lastname: Hauryliuk
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, Munich 81377, Germany Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich 81377, Germany.
authors.forename: Roland
authors.initials: R
authors.lastname: Beckmann
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, Munich 81377, Germany Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich 81377, Germany wilson@lmb.uni-muenchen.de.
authors.forename: Daniel N
authors.initials: DN
authors.lastname: Wilson
mesh_terms: D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D001277:GTP Pyrophosphokinase / Q000737:chemistry / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D006150:Guanine Nucleotides / Q000096:biosynthesis / Q000737:chemistry*; D008025:Ligases / Q000737:chemistry* / Q000235:genetics; D008968:Molecular Conformation; D012343:RNA, Transfer / Q000737:chemistry* / Q000235:genetics; D012270:Ribosomes / Q000737:chemistry* / Q000235:genetics
chemical_list: D006150:Guanine Nucleotides; C018957:guanosine 5'-diphosphate-3'-monophosphate; D012343:RNA, Transfer; D001277:GTP Pyrophosphokinase; D008025:Ligases; C028812:guanosine 3',5'-polyphosphate synthetases