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Updated: Jul 6, 2026

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

Organisms can essentially be classified according to two codon patterns.

T Okayasu¹, K Sorimachi

¹Center of Medical Informatics, Dokkyo Medical University, Mibu, Tochigi 321-0293, Japan.

|April 2, 2008

Summary

All organisms, including bacteria, archaea, and eukaryotes, can be classified into two genome types (AT-type and GC-type) based on codon third position nucleotide content. These types correlate with amino acid concentrations, indicating distinct evolutionary paths.

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Published on: August 16, 2017

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Previous classification of 23 bacteria into S-type (Staphylococcus aureus) and E-type (Escherichia coli) based on amino acid concentrations.
Amino acid composition and nucleotide content are key genomic features.

Purpose of the Study:

To investigate prokaryotic and eukaryotic genome structures using amino acid compositions and nucleotide contents.
To classify a broader range of organisms based on genomic features.

Main Methods:

Cluster analysis of GC content at the third codon position for 112 bacteria, 15 archaea, and 18 eukaryotes.
Calculation of amino acid concentrations and nucleotide contents from complete genomes.
Correlation analysis between amino acid concentrations and nucleotide content.

Main Results:

Classification of 145 organisms into AT-type (high A/T, low G/C) and GC-type (high G/C, low A/T) based on third codon position.
Synchronous reciprocal changes in nucleotide content at the third codon position across organisms.
Differential correlations between amino acid concentrations (Ala, Ile, Lys) and GC content across bacteria, archaea, and eukaryotes, suggesting distinct evolutionary trajectories.

Conclusions:

All organisms are fundamentally classifiable into two groups based on characteristic codon patterns (AT-type and GC-type).
Distinct evolutionary pathways for bacteria, archaea, and eukaryotes are reflected in their genomic composition and amino acid-nucleotide correlations.
Genomic analysis of nucleotide content and amino acid composition provides insights into organismal classification and evolution.