The molecular evolution of cytochrome c in eukaryotes.

Area of Science:

• Molecular Evolution
• Genomics
• Biochemistry

Background:

• Cytochrome c is a crucial protein in eukaryotic electron transport.
• Understanding its evolutionary history provides insights into fundamental biological processes.
• Previous studies were limited by smaller sequence datasets.

Purpose of the Study:

• To analyze a large dataset of cytochrome c sequences to elucidate evolutionary patterns.
• To identify non-randomness in nucleotide and amino acid substitutions.
• To determine the evolutionary rate and variability of cytochrome c genes.

Main Methods:

• Phylogenetic analysis of a comprehensive set of eukaryotic cytochrome c sequences.
• Codon-based analysis to identify patterns of nucleotide and amino acid fixation.
• Assessment of amino acid residue properties and their impact on variability.
• Calculation of the unit evolutionary period.

Main Results:

• Eukaryotic cytochrome c evolved from a common ancestor, with ancestral forms similar to modern ones.
• Codon fixations are non-random, with distinct variability classes observed at nucleotide and amino acid levels.
• Mammalian and plant cytochrome c genes exhibit approximately 12 concomitantly variable codons (covarions).
• Variable codons often encode external residues, while invariable codons frequently encode internal residues.
• Nucleotide replacement patterns show significant non-randomness, influenced by the functional acceptability of resulting amino acid changes.
• The unit evolutionary period for cytochrome c is estimated at ~150 million years per covarion replacement.

Conclusions:

• The evolution of cytochrome c is characterized by non-random processes, strongly influenced by protein structure and function.
• Physicochemical properties of amino acids play a critical role in determining the acceptability of mutations.
• Phylogenetic analysis based on sequence data alone is robust and not biased by prior assumptions of evolutionary relationships.