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A census of protein repeats.
E M Marcotte1, M Pellegrini, T O Yeates
1Molecular Biology Institute, UCLA-DOE Lab of Structural Biology and Molecular Medicine, Los Angeles, CA, P.O. Box 951570, USA.
Journal of Molecular Biology
|October 8, 1999
Summary
Eukaryotic proteins frequently contain internal repeats, unlike prokaryotic ones, suggesting these arose after lineage divergence. This repeat expansion may accelerate protein evolution in eukaryotes.
Area of Science:
- Molecular Biology
- Evolutionary Biology
- Bioinformatics
Background:
- Repetitive amino acid sequences are common in proteins, but their prevalence and origin differ between prokaryotic and eukaryotic organisms.
- Understanding the mechanisms and evolutionary implications of internal protein repeats is crucial for deciphering protein function and evolution.
Purpose of the Study:
- To analyze the occurrence and characteristics of repeating amino acid segments across known protein sequences.
- To investigate the evolutionary origins and functional significance of internal protein repeats, particularly the differences between eukaryotes and prokaryotes.
Main Methods:
- Bioinformatic analysis of all known protein sequences to identify repeating amino acid segments.
- Clustering of repetitive segments into families to compare eukaryotic and prokaryotic repeats.
- Frequency distribution analysis of repeating unit lengths to infer formation mechanisms.
Main Results:
- Internal repeats are found in 14% of proteins, with eukaryotes being three times more likely to possess them than prokaryotes.
- Eukaryotic and prokaryotic repeats show minimal similarity, indicating their independent evolution post-divergence.
- Repetitive sequences are enriched in small, water-soluble residues, and their formation appears driven by recombination.
Conclusions:
- The prevalence of repeats in eukaryotic-specific protein classes suggests their role in specialized eukaryotic functions.
- Recombination is implicated as the primary mechanism for repeat formation, favoring further duplication.
- Error-prone repeat expansion may facilitate faster protein evolution in eukaryotes.