The complete structure of the chloroplast 70S ribosome in complex with translation factor pY

• Published in: The EMBO journal 2017-02, Vol.36 (4), p.475-486
• Main Authors: Bieri, Philipp, Leibundgut, Marc, Saurer, Martin, Boehringer, Daniel, Ban, Nenad
• Format: Article
• Language: English
• Subjects: Algae; Biosynthesis; Botany; Carbon fixation; chloroplast; Chloroplasts; Cryoelectron Microscopy; cryo‐EM; EMBO30; EMBO32; EMBO40; Energy conversion; Models, Molecular; Plastics; Protein synthesis; Ribosomal Proteins - chemistry; Ribosomal Proteins - ultrastructure; ribosome; Ribosomes - chemistry; Ribosomes - ultrastructure; RNA, Ribosomal - chemistry; RNA, Ribosomal - ultrastructure; Spinacia oleracea; translation
• ISSN: 0261-4189; 1460-2075
• DOI: 10.15252/embj.201695959

Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo‐EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid‐specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid‐specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light‐ and temperature‐dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A‐site and P‐site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non‐rotated state, in which the intersubunit bridges to the large subunit are stabilized. Synopsis The first high‐resolution cryo‐EM structure of the chloroplast ribosome sheds light on the role for chloroplast‐specific ribosomal proteins (RPs). The structure further illustrates how protein synthesis is regulated by pY, a translation factor involved in light‐ and temperature‐dependent control of protein synthesis. The complete structure of the chloroplast 70S ribosome is resolved by cryo‐EM at 3.4 Å resolution. The 3D reconstruction reveals the structure of the 4.5S rRNA and shows how the five plastid‐specific RPs bind and stabilize chloroplast‐specific rRNA regions. Plastid‐specific extensions of RPs remodel the mRNA entry and exit site as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle. Translation factor pY binding to the small subunit mRNA channel protects the decoding center, inhibits translation by preventing tRNA binding and locks the small subunit in a non‐rotated state. Graphical Abstract The first high‐r