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Distinct stages of protein evolution as suggested by protein sequence analysis
E N Trifonov1, A Kirzhner, V M Kirzhner
1Department of Structural Biology, The Weizman Institute of Science, Rehovot 76100, Israel. edward.trifonov@weizmann.ac.il
Journal of Molecular Evolution
|October 25, 2001
Summary
The evolution of protein-coding nucleotide sequences began with the triplet code, starting with alanine and glycine. Protein evolution progressed through minigene fusion, loop formation, and gene fusion, leading to modern multidomain proteins.
Area of Science:
- Biochemistry
- Molecular Biology
- Evolutionary Biology
Background:
- Protein evolution traces back to the advent of the triplet code, a fundamental concept in molecular biology.
- Amino acid appearance and triplet code evolution have been reconstructed using various criteria.
- Early protein structures likely involved short polypeptide chains encoded by complementary mRNA strands.
Purpose of the Study:
- To reconstruct the chronological order of amino acid appearance and triplet code evolution.
- To investigate the structural evolution of proteins from short chains to complex folds.
- To identify evolutionary stages and their underlying molecular mechanisms.
Main Methods:
- Analysis of 40 different ranking criteria and hypotheses for chronological reconstruction.
- Identification of complementary codon pairs and their associated amino acid alphabets (Glycine and Alanine alphabets).
- Autocorrelation analysis of protein sequences from prokaryotic genomes to detect structural patterns.
Main Results:
- The GGC and GCC codons for glycine and alanine, respectively, appeared first, forming complementary pairs.
- Amino acids were divided into two alphabets (Glycine and Alanine) based on central purines or pyrimidines in codons.
- Protein sequences exhibit weak oscillations indicating mosaic structures from minigene fusion and preferred loop sizes (25-30 residues) stabilized by hydrophobic interactions.
Conclusions:
- Protein evolution progressed through stages: triplet code establishment, minigene fusion forming mosaic structures, loop formation stabilized by hydrophobic interactions, and gene fusion leading to multidomain proteins.
- The optimal ring closure for DNA likely dictated the size of early protein folds (100-200 amino acids).
- Recombinational gene splicing likely emerged after DNA circularization.