Codon preference is but an illusion created by the construction principle of coding sequences.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Modern coding sequences exhibit characteristics of a periodic-to-chaotic transition.
• Two related sequences, lens alpha A-crystallin and small heat shock protein, were analyzed.
• The original repeating units in these sequences were heptameric.

Purpose of the Study:

• To investigate the structural basis of codon preference.
• To determine if codon usage is driven by sequence construction or natural selection.
• To analyze the recurrence patterns of base trimers within coding sequences.

Main Methods:

• Analysis of coding sequences for lens alpha A-crystallin and small heat shock protein.
• Identification and quantification of recurring heptameric units.
• Frequency analysis of base trimers within these units.
• Correlation of trimer frequency with codon usage for specific amino acids.

Main Results:

• Base trimers within heptameric units recurred significantly more often than others.
• In crystallin sequences, CTG, TCT, and TCC trimers were highly frequent, correlating with leucine and serine encoding.
• In small heat shock protein, AGC was prominent, correlating with serine encoding.
• Codon usage directly reflected the frequency of constituent trimers.

Conclusions:

• Codon preference is a consequence of the inherent construction principles of coding sequences.
• The observed codon usage patterns are not primarily driven by natural selection.
• Sequence periodicity and repeating units are key determinants of codon usage bias.