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Alterations in rRNA-mRNA interaction during plastid evolution

Kyungtaek Lim1, Ichizo Kobayashi1, Kenta Nakai2

  • 1Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato-ku, Tokyo, JapanThe Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.

Molecular Biology and Evolution
|April 9, 2014
PubMed

Insights

Plastids retain Shine-Dalgarno interactions for translation initiation, with some lineages evolving altered interactions. This demonstrates the adaptability of the translation machinery during organelle evolution.

Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Genomics

Background:

  • Translation initiation in prokaryotes relies on Shine-Dalgarno (SD) interactions between ribosomal RNA and mRNA.
  • This interaction involves base pairing between the 3'-tail of small subunit rRNA (core motif: 3'CCUCC) and a complementary sequence in the mRNA's 5'-untranslated region.

Purpose of the Study:

  • To investigate the evolutionary fate of Shine-Dalgarno interactions during the transition of cyanobacterial endosymbionts to modern plastids.
  • To analyze the conservation and variation of SD interactions across diverse plastid lineages.

Main Methods:

  • Analysis of complete plastid genome sequences from various lineages.
  • Comparative genomics to identify conserved and divergent sequences in rRNA and mRNA involved in translation initiation.

Main Results:

  • Most plastids maintain SD interactions, though usage varies significantly.
  • SD interactions were lost in plastids of Chlorophyta, Euglenophyta, and Chromerida/Apicomplexa, correlating with reductive evolution.
  • An altered SD interaction (3'CCCU/5'GGGA or 3'CUUCC/5'GAAGG) replaced the classical one (3'CCUCC/5'GGAGG) in some lineages, involving coordinated sequence changes in rRNA and mRNA.

Conclusions:

  • Plastid evolution exhibits plasticity in translation initiation, with evidence of both retention and modification of SD interactions.
  • Coevolution between the rRNA motif and mRNA signal highlights the dynamic nature of the translational machinery.
  • Intermediate stages suggest a gradual evolutionary process for the altered SD interactions in Chlorophyta and Euglenophyta.
Keywords:
Shine–Dalgarno sequencechloroplastendosymbiosisribosometranslation

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