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Updated: Jun 13, 2026

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Published on: June 24, 2019
Gene functionality's influence on the second codon: A large-scale survey of second codon composition in three domains
Sen-Lin Tang1, Bill C H Chang, Saman K Halgamuge
1Biodiversity Research Center, Academia Sinica, Taipei, Taiwan. sltang@gate.sinica.edu.tw
The second codon influences protein production and processing. Its amino acid composition varies based on gene function, impacting cell envelope, translation, and energy metabolism processes.
Area of Science:
- Molecular Biology
- Genomics
- Biochemistry
Background:
- The second codon of a transcript has crucial roles beyond amino acid encoding, including translation efficiency and protein maturation.
- These diverse functions impose complex selection pressures on the second codon's sequence composition.
Purpose of the Study:
- To investigate the biological significance of different second codon compositions.
- To analyze the relationship between second codon composition and gene function across various organisms.
Main Methods:
- Conducted a systematic survey of second codon composition.
- Analyzed data from 442 diverse genomes spanning three domains of life.
Main Results:
- Observed an amino acid bias in the second codon that correlates with specific protein functions.
- Found that common amino acids (Serine, Alanine, Lysine, Threonine) are avoided in cell envelope genes but preferred in translation and energy metabolism genes.
Conclusions:
- Gene product function is a significant determinant of second codon composition.
- The specific amino acid at the second codon position is influenced by the gene's role within the cell.
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