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Rare codons in E. coli and S. typhimurium signal sequences.

D M Burns, I R Beacham

|September 23, 1985

Summary

Researchers analyzed codon usage in protein signal sequences, finding a bias in rare codons for hydrophobic amino acids. This may influence protein secretion by delaying translation during the secretion process.

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Area of Science:

Molecular Biology
Genetics
Protein Biochemistry

Background:

Signal sequences are crucial for protein localization, directing proteins to specific cellular compartments or for secretion.
Leader peptides, rich in hydrophobic residues, are integral parts of signal sequences.
Codon usage bias, the non-random selection of codons, can impact translation efficiency and protein folding.

Purpose of the Study:

To investigate codon usage patterns within signal sequences of secreted and inner-membrane proteins.
To compare codon usage in signal sequences with that of the mature protein coding sequences.
To explore the potential role of codon usage bias in the signal sequence on protein secretion.

Main Methods:

Analysis of codon usage in 27 genes encoding proteins with leader peptides.
Comparison of codon usage in signal sequences versus mature protein coding sequences.
Identification of biases in the usage of rare codons for specific amino acids.

Main Results:

A significant bias in the usage of rare codons was observed for two of the three hydrophobic amino acids with available rare codons.
Hydrophobic residues are predominant in leader peptides, suggesting a concentration of rare codons in these regions.
The observed rare codon bias in signal sequences is linked to the high proportion of hydrophobic amino acids.

Conclusions:

The concentration of rare codons within signal sequences, particularly in hydrophobic regions, may play a role in regulating protein secretion.
This rare codon bias could potentially delay translation, influencing the efficiency or mechanism of protein translocation across membranes.
The findings suggest an evolutionary role for codon usage bias in the signal sequence for optimizing the protein secretion process.

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