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Updated: Jun 14, 2026
10:37
Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs
Published on: May 10, 2018
Dynamic evolution of translation initiation mechanisms in prokaryotes
So Nakagawa1, Yoshihito Niimura, Kin-ichiro Miura
1Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima 411-8540, Japan.
Summary
The Shine-Dalgarno sequence is not universally required for prokaryotic translation initiation. Alternative mechanisms, like ribosomal protein S1 (RPS1) mediation or leaderless mRNA, are utilized, indicating dynamic evolutionary changes in translation initiation.
Area of Science:
- Molecular Biology
- Evolutionary Biology
- Genomics
Background:
- Prokaryotic translation initiation typically relies on the Shine-Dalgarno (SD) sequence interacting with 16S ribosomal RNA.
- Alternative mechanisms exist, including those mediated by ribosomal protein S1 (RPS1) and leaderless mRNA, bypassing the need for an SD sequence.
Purpose of the Study:
- To investigate the universality of the SD sequence in prokaryotic translation initiation.
- To understand the evolutionary dynamics of translation initiation mechanisms across different prokaryotic phyla.
Main Methods:
- Bioinformatic analysis of 277 prokaryotic species (249 eubacteria, 28 archaebacteria) to identify SD sequences.
- Development of an SD index, accounting for GC content variations, to quantify SD sequence prevalence.
- Comparative analysis of SD sequence conservation and loss across prokaryotic phyla.
Main Results:
- SD sequence prevalence (SD index) varies significantly among prokaryotic species but remains consistent within phyla.
- While the anti-SD sequence is conserved, the SD sequence has been independently lost multiple times across different phyla.
- Evidence suggests increased reliance on RPS1-mediated or leaderless mRNA mechanisms in phyla lacking SD sequences.
- Some species, like Cyanobacteria, show potential acquisition of novel translation initiation mechanisms.
Conclusions:
- Prokaryotic translation initiation mechanisms are not static and have undergone dynamic evolutionary changes.
- The loss and potential acquisition of translation initiation strategies highlight the adaptability of prokaryotic gene expression.
- Understanding these diverse mechanisms is crucial for comprehending prokaryotic evolution and gene regulation.
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