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Published on: July 11, 2013
Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of
Prashanth Vishwanath1, Paola Favaretto, Hyman Hartman
1BioMolecular Engineering Research Center, Boston University, 36 Cummington St., Boston, MA 02215, USA.
Molecular Phylogenetics and Evolution
|November 4, 2004
Summary
Prokaryotic and eukaryotic ribosomal proteins reveal distinct sequence blocks, suggesting a common ancestor followed by divergence after a major evolutionary bottleneck. Eukaryotic proteins align more closely with archaeal counterparts.
Area of Science:
- Evolutionary biology
- Molecular evolution
- Genomics
Background:
- Ribosomal proteins in Bacteria, Archaea, and Eukaryota exhibit unique sequence block patterns.
- These patterns have significant implications for understanding early life evolution.
- The structure of these blocks is not consistently linked to specific functional or structural features.
Purpose of the Study:
- To investigate the evolutionary relationships between prokaryotic and eukaryotic ribosomal proteins.
- To analyze the implications of sequence block structures on phylodomain evolution.
- To explore the evolutionary origin of eukaryotes in relation to prokaryotes.
Main Methods:
- Amino acid sequence alignments of orthologous ribosomal proteins across Bacteria, Archaea, and Eukaryota.
- Phylogenetic analysis of ribosome-associated proteins.
- Comparative analysis of sequence block patterns in different protein types.
Main Results:
- Cross-domain alignments reveal universal, bacterial-specific, and archaeal-specific sequence blocks.
- Eukaryotic cytoplasmic ribosomal proteins with bacterial and archaeal orthologs exclusively match archaeal block structures.
- The phylodomain-specific block pattern is observed in other protein synthesis-related proteins but not in metabolic enzymes.
- Phylogenetic analysis indicates eukaryotes originated around the same time as the divergence event and show closer ties to crenarchaeal proteins.
Conclusions:
- Modern Bacteria and Archaea share a common ancestor, but their distinct sequence blocks suggest divergence from unique, phylodomain-specific lineages after this ancestor.
- A significant evolutionary bottleneck event after the development of the translation apparatus is the most plausible explanation for the observed pattern.
- The diversity of prokaryotes reflects post-bottleneck divergent evolution.
- Eukaryotic evolution is closely linked to archaeal lineages, particularly crenarchaea.
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