title: Mechanisms of ribosome stalling by SecM at multiple elongation steps.
abstract: Regulation of translating ribosomes is a major component of gene expression control network. In Escherichia coli, ribosome stalling by the C-terminal arrest sequence of SecM regulates the SecA-dependent secretion pathway. Previous studies reported many residues of SecM peptide and ribosome exit tunnel are critical for stalling. However, the underlying molecular mechanism is still not clear at the atomic level. Here, we present two cryo-EM structures of the SecM-stalled ribosomes at 3.3-3.7 Å resolution, which reveal two different stalling mechanisms at distinct elongation steps of the translation cycle: one is due to the inactivation of ribosomal peptidyl-transferase center which inhibits peptide bond formation with the incoming prolyl-tRNA; the other is the prolonged residence of the peptidyl-RNA at the hybrid A/P site which inhibits the full-scale tRNA translocation. These results demonstrate an elegant control of translation cycle by regulatory peptides through a continuous, dynamic reshaping of the functional center of the ribosome.
authors.affiliation: State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
authors.forename: Xijiang
authors.initials: X
authors.lastname: Pan
authors.affiliation: Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
authors.forename: Kaige
authors.initials: K
authors.lastname: Yan
authors.affiliation: State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
authors.forename: Shan
authors.initials: S
authors.lastname: Sun
authors.affiliation: Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Gao
authors.affiliation: State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
authors.forename: Sen-Fang
authors.initials: SF
authors.lastname: Sui
mesh_terms: D020285:Cryoelectron Microscopy; D004926:Escherichia coli / Q000235:genetics / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D010441:Peptide Chain Elongation, Translational; D012270:Ribosomes / Q000378:metabolism* / Q000648:ultrastructure; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; C497347:SecM protein, E coli; D014157:Transcription Factors
keywords: E. coli; biophysics; electron microscopy; ribosome stalling; single particle analysis; structural biology