Chloroplast-encoded small subunit extensions reshape the Chlamydomonas chlororibosome

Chloroplast ribosomes (chlororibosomes) synthesize the core protein components of the photosynthetic apparatus, yet their structural diversity outside flowering plants remains largely unexplored. Here we combine in situ cryo-electron tomography with single-particle cryo-electron microscopy to determine the structure of the chlororibosome from the unicellular green alga Chlamydomonas reinhardtii. Subtomogram averaging of chlororibosomes in their native environment, resolved to ~5 Å and in distinct translational states, reveals particles both free in the stroma and flexibly tethered to thylakoid membranes. These in situ reconstructions uncover an additional 'arm' domain on the small subunit. High-resolution single-particle structures of isolated chlororibosomes resolved to ~2.5 Å, in states bound either to the inhibitory translation factor pY or to a nascent chain-linked P-site transfer RNA, reveal that this domain is built primarily from extensive chloroplast-encoded insertions and extensions of conserved small subunit proteins, supported by chlororibosome-specific ribosomal proteins. The arm domain is located around the mRNA entry and exit channels, suggesting a role in stabilizing the mRNA trajectory through the small subunit and organizing chloroplast polysomes. Together, these data reveal the unexpected structural variation of algal chlororibosomes and suggest that chloroplast translation has diversified substantially even among relatively closely related photosynthetic lineages.