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Reductive evolution of proteomes and protein structures
Minglei Wang1, Charles G Kurland, Gustavo Caetano-Anollés
1Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.
Summary
Protein linker sequences in eukaryotes are significantly longer than those in prokaryotes. This difference, not due to protein domains, suggests reductive evolution in prokaryotic linker lengths correlated with genome coding capacity.
Area of Science:
- Genomics
- Molecular Biology
- Evolutionary Biology
Background:
- Orthologous protein families are notably longer in Eukarya compared to Bacteria and Archaea.
- Protein length disparities between superkingdoms have been observed but not fully explained.
Purpose of the Study:
- To investigate the structural basis for protein length differences across superkingdoms.
- To determine the evolutionary dynamics of protein linker and domain sequences in relation to proteome diversity.
Main Methods:
- Analysis of protein structures across 745 genomes.
- Comparison of linker and domain sequence lengths in Eukaryotes, Bacteria, and Archaea.
- Correlation of linker lengths with genome coding sequence (CDS) as a measure of proteome diversity.
Main Results:
- Prokaryotic (Bacteria and Archaea) linker sequences are substantially shorter than eukaryotic ones.
- Linker lengths in prokaryotes show a clear proportional evolution with genome CDS, indicating reductive evolution.
- Eukaryotic linker lengths are larger than expected and do not correlate with CDS, while domain lengths remain relatively constant across all groups.
Conclusions:
- Protein length differences are primarily driven by variations in non-domain linker sequences.
- Prokaryotic linker evolution appears reductive and linked to proteome diversity (CDS).
- Eukaryotic linker evolution does not follow the same reductive pattern observed in prokaryotes.
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01:24Protein Organization
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The primary structure of a protein is its amino acid sequence.
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