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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
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Evolutionary Flexibility of Ribosome Biogenesis in Bacteria.

Kazuaki Amikura1, Shun Ichi Ishii2, Yoshihiro Shimizu3

  • 1Geobiology and Astrobiology Laboratory, RIKEN Pioneering Research Institute (PRI), Wako, Saitama, Japan.

Molecular Biology and Evolution
|November 24, 2025
PubMed
Summary
This summary is machine-generated.

Candidate Phyla Radiation bacteria possess fewer ribosome biogenesis factors, suggesting early evolutionary divergence. Ribosomal structural changes correlate with reduced factors, indicating co-evolution.

Keywords:
CPR bacteriaco-evolutionrRNAribosome biogenesis

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Area of Science:

  • Microbiology
  • Evolutionary Biology
  • Genomics

Background:

  • Ribosomes are crucial for protein synthesis and require numerous biogenesis factors for assembly.
  • Understanding the diversity of ribosome biogenesis is key to comprehending bacterial evolution.
  • Candidate Phyla Radiation (CPR) bacteria exhibit reduced genomes and smaller ribosomes, hinting at unique biological adaptations.

Purpose of the Study:

  • To investigate the evolutionary diversity of ribosome biogenesis factors across bacterial phyla.
  • To characterize the repertoire of ribosome biogenesis factors in Candidate Phyla Radiation (CPR) bacteria.
  • To explore the relationship between ribosomal structure and the number of biogenesis factors.

Main Methods:

  • Analysis of over 30,000 bacterial genomes.
  • Comparative genomics to identify and quantify ribosome biogenesis factors.
  • Correlation analysis between ribosomal structural elements and factor presence.

Main Results:

  • CPR bacteria possess approximately half the average number of ribosome biogenesis factors compared to other bacteria.
  • Essential factors like der, obgE, and rbfA are conserved in only 20%-70% of CPR genomes.
  • Ribosomal structural modifications correlate with a reduced set of biogenesis factors.

Conclusions:

  • Ribosome biogenesis is more flexible than previously thought.
  • The reduced genome size, small cell size, and early divergence of CPR bacteria likely contribute to their unique ribosome biogenesis factor repertoires.
  • Co-evolution between ribosomal structure and biogenesis factors is evident in CPR bacteria.