bims-tricox 2023-01-01 papers

Issue of 2023‒01‒01
two papers selected by
Yash Verma
University of Delhi South Campus

Nucleic Acids Res. 2022 Dec 30. pii: gkac1211. [Epub ahead of print]

Ratchet, swivel, tilt and roll: a complete description of subunit rotation in the ribosome.

Asem Hassan, Sandra Byju, Frederico Campos Freitas, Claude Roc, Nisaa Pender, Kien Nguyen, Evelyn M Kimbrough, Jacob M Mattingly, Ruben L Gonzalez, Ronaldo Junio de Oliveira, Christine M Dunham, Paul C Whitford.

Protein synthesis by the ribosome requires large-scale rearrangements of the 'small' subunit (SSU; ∼1 MDa), including inter- and intra-subunit rotational motions. However, with nearly 2000 structures of ribosomes and ribosomal subunits now publicly available, it is exceedingly difficult to design experiments based on analysis of all known rotation states. To overcome this, we developed an approach where the orientation of each SSU head and body is described in terms of three angular coordinates (rotation, tilt and tilt direction) and a single translation. By considering the entire RCSB PDB database, we describe 1208 fully-assembled ribosome complexes and 334 isolated small subunits, which span >50 species. This reveals aspects of subunit rearrangements that are universal, and others that are organism/domain-specific. For example, we show that tilt-like rearrangements of the SSU body (i.e. 'rolling') are pervasive in both prokaryotic and eukaryotic (cytosolic and mitochondrial) ribosomes. As another example, domain orientations associated with frameshifting in bacteria are similar to those found in eukaryotic ribosomes. Together, this study establishes a common foundation with which structural, simulation, single-molecule and biochemical efforts can more precisely interrogate the dynamics of this prototypical molecular machine.

DOI: https://doi.org/10.1093/nar/gkac1211

Nucleic Acids Res. 2022 Dec 30. pii: gkac1208. [Epub ahead of print]

Polyribosomes of circular topology are prevalent in mammalian cells.

Timur N Baymukhametov, Dmitry N Lyabin, Yury M Chesnokov, Ivan I Sorokin, Evgeniya V Pechnikova, Alexander L Vasiliev, Zhanna A Afonina.

Polyribosomes, the groups of ribosomes simultaneously translating a single mRNA molecule, are very common in both, prokaryotic and eukaryotic cells. Even in early EM studies, polyribosomes have been shown to possess various spatial conformations, including a ring-shaped configuration which was considered to be functionally important. However, a recent in situ cryo-ET analysis of predominant regular inter-ribosome contacts did not confirm the abundance of ring-shaped polyribosomes in a cell cytoplasm. To address this discrepancy, here we analyzed the cryo-ET structure of polyribosomes in diluted lysates of HeLa cells. It was shown that the vast majority of the ribosomes were combined into polysomes and were proven to be translationally active. Tomogram analysis revealed that circular polyribosomes are indeed very common in the cytoplasm, but they mostly possess pseudo-regular structures without specific inter-ribosomal contacts. Although the size of polyribosomes varied widely, most circular polysomes were relatively small in size (4-8 ribosomes). Our results confirm the recent data that it is cellular mRNAs with short ORF that most commonly form circular structures providing an enhancement of translation.

DOI: https://doi.org/10.1093/nar/gkac1208