Codon usage clusters correlation: towards protein solubility prediction in heterologous expression systems in E....

Area of Science:

• Biotechnology
• Molecular Biology
• Bioinformatics

Background:

• Soluble recombinant protein production is vital for industrial applications and scientific research.
• Protein aggregation due to misfolding remains a significant challenge in recombinant protein expression.
• Understanding factors influencing protein solubility is key to improving protein design and production.

Purpose of the Study:

• To quantitatively investigate the relationship between codon usage and the expression and solubility of Bizionia argentinensis proteins.
• To identify parameters predicting protein solubility based on codon usage analysis.
• To explore the role of codon usage conservation in modulating protein folding and translation.

Main Methods:

• Utilized the %MinMax algorithm to define parameters comparing codon usage clusters between host and target genes.
• Analyzed expression levels and solubility of Bizionia argentinensis proteins.
• Correlated codon usage features with protein expression and solubility across two independent datasets.

Main Results:

• A significant negative correlation was found between the absolute difference in %MinMax frequencies and protein expression levels.
• A strong positive correlation was observed between codon usage cluster conservation and protein solubility.
• This correlation was more pronounced in codon usage clusters associated with less compact protein secondary structures.

Conclusions:

• Codon usage conservation is a significant predictor of protein solubility.
• The findings suggest that codon usage influences translation rate and co-translational folding.
• This research provides valuable tools for optimizing recombinant protein design and production.