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Focus on helical polyribosomes

At the top: Helical structure of the polyribosome, in blue the 60S subunits facing outwards. At the bottom : Details of protein interactions between the exit site of the mRNA at a ribosome (i), and the entry site of the mRNA on the following ribosome (i + 1). These details show a continuity of the channel that contains the mRNA (red dotted line), from a ribosome to another without forming loops, which allows it to be protected inside.

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.

Myasnikov AG(1), Afonina ZA(2), Ménétret JF(1), Shirokov VA(2), Spirin AS(2), Klaholz BP(1).

Nat Commun Nov. 7, 2014

Nov. 7, 2014

Key elements of protein synthesis, ribosomes are sometimes positioned like beads on a string on the messenger RNA to amplify the effectiveness of translation. While little information was available about the precise structure of this assembly, microscopists and crystallographers of Bruno Klaholz’s team managed to determine its precise configuration in 3 dimensions, providing new information on the mechanisms of translation. These results are published November 7th in the journal Nature Communications.


Protein synthesis under the microscope
Protein synthesis is carried out in several stages. Thanks to the RNA polymerase, the DNA molecule is first transcribed into messenger RNA (mRNA), which is in turn translated into protein by the ribosomes. Electron microscopy enables to display all of these steps and has shown that ribosomes sometimes assemble "as beads on a string" on the same RNA molecule, in order to simultaneously translate it, and thereby produce large amounts of proteins. This assembly is called a "polyribosome". However, electron microscopy in the past only allowed the observation of a zigzag structure in two dimensions  whose meaning remained obscure for the last 40 years.


A helical structure
In this new study, the researchers managed to determine the complete 3-dimensional structure of a 100 MDa assembly, comprising no less than 23 ribosomes on the same mRNA molecule. This has become possible by cryo electron tomography, in which the object is observed from different angles before being reconstituted by computational 3D reconstruction. Coupled with detailed structural knowledge on the ribosome alone from X-ray crystallography and cryo-EM, these new data were used to determine very accurately the 3-dimensional structure of the polyribosome and of the different interactions between ribosomes that it comprises, thus visualizing in 3D the starting, producing and ending steps of protein synthesis. Notably, the researchers showed that ribosomes are assembled as a left-handed supramolecular helix and form a continuous channel, into which the mRNA molecule is embedded. Separated by about forty nucleotides, ribosomes are positioned in a specific orientation, the small subunit (40S) inwards, and the large one (60S), which allows the output of the synthesized protein, outwards. In this very compact structure, interactions between ribosomes are numerous (30% of their surface), thereby enhancing the stability of the helix.


Efficiency and synchronization
This very dense structure raises the question of whether the mRNA could be overloaded, and thanks to kinetic studies, the researchers also revealed that the efficiency of translation is optimal with 8 ribosomes on the same mRNA molecule. When an overload of ribosomes occurs it could put protein synthesis on standby, with the possibility of reactivating it rapidly when needed, such as in neuronal synapses.
Beyond the structural aspects, the researchers found that active ribosomes were generally all in the same state of the translation process. This homogeneity raises the hypothesis of cooperation between ribosomes which would be able to work together in a synchronized manner.


These findings shed new light on the molecular machinery of the ribosome arranged as chains on the messenger RNA, and enlarge the knowledge on the vital and highly complex process of protein synthesis.

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