Predicting Rare Codons in Protein Families
Author Information
Author(s): Michael Widmann, Marie Clairo, Jürgen Dippon, Jürgen Pleiss
Primary Institution: Institute of Technical Biochemistry, Stuttgart, Germany
Hypothesis
Critical rare codons can be predicted by comparing the codon usage of homologous proteins in a multisequence alignment.
Conclusion
A systematic analysis of multisequence alignments can predict rare codons that may impact protein expression, suggesting that these codons should not be replaced with more frequent ones.
Supporting Evidence
- The method successfully predicts functionally relevant codons in fatty acid binding protein and chloramphenicol acetyltransferase.
- Most genes contain at least one putative rare codon rich region.
- Rare codons located near to those regions should be excluded in approaches to improve protein expression.
Takeaway
Some parts of genes have special codes that help proteins fold correctly. If we change these codes to more common ones, it might make the proteins not work well.
Methodology
The study analyzed multisequence alignments of homologous protein families to identify rare codon rich regions.
Limitations
The analysis may not predict functionally relevant rare codons located in highly variable regions.
Digital Object Identifier (DOI)
Want to read the original?
Access the complete publication on the publisher's website