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Published on: June 24, 2019
Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome
Uttam Roymondal1, Shibsankar Das, Satyabrata Sahoo
1Department of Mathematics, Raidighi College, South 24 Parganas, Raidighi, West Bengal, India.
Summary
We developed a new gene expression measure using relative codon bias (RCB) to predict gene expression levels. This method, relative codon bias strength (RCBS), successfully predicts gene expression in E. coli and reveals shorter genes are expressed at higher levels.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Gene expression levels are crucial for cellular function.
- Existing codon usage measures may not fully capture gene expressivity.
- Understanding codon preference is key to predicting gene expression.
Purpose of the Study:
- To introduce a novel gene expression measure based on relative codon bias (RCB).
- To assess the correlation between RCB and gene expression levels.
- To analyze the relationship between gene expression and protein length in E. coli.
Main Methods:
- Definition and calculation of relative codon bias strength (RCBS).
- Application of RCBS to the Escherichia coli (E. coli) genome.
- Correlation analysis between RCBS, protein length, and existing expression data.
Main Results:
- RCBS effectively predicts gene expression levels in E. coli.
- A significant positive correlation was found between RCBS and protein abundance.
- A surprising inverse correlation between gene length and expression level was observed.
Conclusions:
- RCBS is a reliable indicator of gene expression levels.
- The findings suggest natural selection favors higher expression of shorter genes.
- The method provides a valuable tool for studying cell physiology and gene regulation.
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