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CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern.

Gabriel Wright1, Anabel Rodriguez2, Jun Li3

  • 1Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, Indiana, USA.

Protein Science : a Publication of the Protein Society
|November 5, 2021
PubMed
Summary
This summary is machine-generated.

Synonymous codon usage impacts protein production and folding. The CHARMING algorithm optimizes mRNA sequences for heterologous gene expression by harmonizing codon usage.

Keywords:
aggregationco-translational protein foldingheterologous gene expressionmisfoldingprotein synthesisribosometranslation

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genetics

Background:

  • Synonymous codon usage, once considered silent, significantly influences functional protein production, including transcription, mRNA stability, translation, and protein folding.
  • Sub-optimal codons play a crucial role in co-translational protein folding, a process increasingly recognized for its impact on protein function.
  • Conserved synonymous codon usage patterns across evolution highlight their biological significance.

Purpose of the Study:

  • To develop a robust and versatile algorithm for designing mRNA sequences to optimize heterologous gene expression.
  • To address the challenges of differing synonymous codon usage patterns between organisms in gene expression contexts.
  • To provide a tool for codon harmonization tasks in molecular biology and biotechnology.

Main Methods:

  • Development of the CHARMING (Codon HARMonizING) algorithm.
  • Implementation as a downloadable Python script and a web portal.
  • Application of the algorithm for designing optimized mRNA sequences.

Main Results:

  • CHARMING provides a method to harmonize synonymous codon usage for improved heterologous gene expression.
  • The algorithm facilitates the design of mRNA sequences tailored to specific expression hosts.
  • Demonstrated utility in various codon harmonization applications.

Conclusions:

  • Synonymous codon usage is a critical factor in functional protein production and can be manipulated for enhanced gene expression.
  • The CHARMING algorithm offers a powerful solution for optimizing mRNA sequences in heterologous systems.
  • This tool has broad applicability in synthetic biology, protein engineering, and genetic research.