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Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

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Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes.

J R Lobry¹, A Necşulea

¹Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), France. lobry@biomserv.univ-lyon1.fr <lobry@biomserv.univ-lyon1.fr>

|September 23, 2006

Summary

Synonymous codon usage in prokaryotes varies with growth temperature. While Arg codons discriminate thermophiles, the link between codon bias and high-temperature growth is not definitively proven, even with psychrophiles included.

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Area of Science:

Microbial genomics
Molecular evolution
Extremophile biology

Background:

Synonymous codon usage in prokaryotes is linked to growth temperature.
Previous research suggests selective pressure related to temperature drives codon bias in (hyper)thermophiles and mesophiles.

Purpose of the Study:

To analyze variations in synonymous codon usage across a broad range of prokaryotic species and growth temperatures.
To investigate whether selective pressure on codon usage operates similarly at low growth temperatures (psychrophiles) as at high temperatures.

Main Methods:

Updated analysis of synonymous codon usage variation with growth temperature.
Inclusion of a wide taxonomic range and diverse growth temperatures, including psychrophilic species.
Factorial map analysis of synonymous codon usage patterns.

Main Results:

Synonymous codon usage for Arginine (Arg) codons (AGG, AGA, CGT) significantly discriminates between (hyper)thermophilic and non-thermophilic species.
An Archaeal psychrophile unusually clustered with thermophilic species on the codon usage factorial map.
Other psychrophilic species clustered with mesophilic species.

Conclusions:

The observed differences in synonymous codon usage between (hyper)thermophilic and non-thermophilic prokaryotes are not solely attributable to selective pressure linked to high-temperature growth.
The atypical codon usage pattern of one psychrophile suggests complex evolutionary factors beyond simple temperature adaptation.