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Ribosomes01:27

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Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
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The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
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Prokaryote translation is a complex, highly coordinated process that converts genetic information from mRNA into functional proteins. It involves three stages: initiation, elongation, and termination, each facilitated by specific molecular components.Initiation of TranslationThe process begins with the assembly of the ribosomal subunits and initiation factors on the mRNA. In bacteria, the 30S ribosomal subunit recognizes the Shine-Dalgarno sequence in the mRNA, a conserved region upstream of...
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Bacterial cells were initially considered simple, randomly organized structures lacking a cytoskeleton. However, the discovery of cytoskeleton homologs in bacteria led to the change of this opinion. Bacterial cytoskeletal filaments regulate the cell shape, cell polarity, cell division, and partitioning of plasmids during cell division. It was later discovered that bacterial cytoskeletal proteins, mainly actin and tubulin homologs, are diverse compared to their eukaryotic counterparts. On the...
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Assembly landscape for the bacterial large ribosomal subunit.

Kai Sheng1, Ning Li1, Jessica N Rabuck-Gibbons1,2

  • 1Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.

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|August 26, 2023
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Summary

Bacterial ribosome assembly is fast but difficult to study. Researchers used cryo-electron microscopy to map the assembly pathway of the 50S ribosomal subunit, revealing key intermediate structures and folding units.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Microbiology

Background:

  • Bacterial ribosome biogenesis is a rapid and essential process.
  • Studying ribosome assembly intermediates is challenging due to their low abundance.

Purpose of the Study:

  • To structurally characterize intermediates in the assembly of the 50S ribosomal subunit in E. coli.
  • To elucidate the hierarchy of RNA-protein cooperative folding units during ribosome biogenesis.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) with iterative subclassification.
  • Principal Component Analysis-Uniform Manifold Approximation and Projection-Hierarchical Density-Based Spatial Clustering of Applications with Noise (PCA-UMAP-HDBSCAN) for dimensionality reduction and cluster picking.

Main Results:

  • Identified and structurally characterized a series of intermediates spanning the 50S ribosomal subunit assembly pathway.
  • Revealed the identity and hierarchical organization of cooperative folding units (RNA and protein components).
  • Generated a comprehensive assembly map for the 50S subunit.

Conclusions:

  • Bacterial 50S ribosomal subunit assembly is a co-transcriptional process with inherent flexibility.
  • The identified assembly map provides mechanistic insights into efficient ribosome biogenesis under varying growth conditions.