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Updated: Jun 5, 2026
06:29
Studying Protein Import into Chloroplasts Using Protoplasts
Published on: December 10, 2018
Pentatricopeptide repeat proteins constrain genome evolution in chloroplasts.
Michael L Hayes1, R Michael Mulligan
1Developmental and Cell Biology, University of California, Irvine, USA.
Molecular Biology and Evolution
|January 26, 2011
Summary
Plant pentatricopeptide repeat proteins (PPRs) constrain chloroplast genome evolution by preserving essential RNA cis-elements. This organellar dependence limits evolutionary changes in RNA processing sites.
Area of Science:
- Molecular Biology
- Plant Science
- Genomics
Background:
- Higher plants possess numerous pentatricopeptide repeat proteins (PPRs) crucial for RNA processing.
- Many PPR proteins target organelles (chloroplasts, mitochondria) and regulate organellar gene expression.
- RNA binding by PPRs is established, with known cis-element sequences.
Purpose of the Study:
- To investigate the evolutionary constraints on RNA cis-elements recognized by PPR proteins in chloroplast genomes.
- To analyze sequence conservation patterns within and around PPR-bound cis-elements.
- To understand the impact of PPR gene family expansion on organelle genome evolution.
Main Methods:
- Analysis of cis-element sequence changes using pairwise nucleotide substitution frequency, indel frequency, and maximum likelihood (ML) phylogenetic distances.
- Comparison of sequences around chloroplast editing sites versus homologous sequences with genomic T (lacking editing).
- Investigation of a pseudogenized PPR gene linked to a non-essential editing site.
Main Results:
- Cis-elements recognized by PPRs are highly conserved within the chloroplast genome compared to surrounding sequences.
- Sequences around RNA editing sites show significantly higher conservation than homologous sequences with genomic T.
- A PPR gene lost its function (became a pseudogene) after an editing site became unnecessary, indicating evolutionary adaptation.
Conclusions:
- Organellar gene expression's reliance on nuclear-encoded PPR proteins imposes strong evolutionary constraints on RNA processing cis-elements.
- These constraints significantly shape the evolution of plant organelle genomes.
- The expansion of the PPR gene family has profoundly influenced plant organelle genome evolution.
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