Expression of codon optimized genes in microbial systems: current industrial applications and perspectives

Abstract

The efficient production of functional proteins in heterologous hosts is one of the major bases of modern biotechnology. Unfortunately, many genes are difficult to express outside their original context. Due to their apparent “silent” nature, synonymous codon substitutions have long been thought to be trivial. In recent years, this dogma has been refuted by evidence that codon replacement can have a significant impact on gene expression levels and protein folding. In the past decade, considerable advances in the speed and cost of gene synthesis have facilitated the complete redesign of entire gene sequences, dramatically improving the likelihood of high protein expression. This technology significantly impacts the economic feasibility of microbial-based biotechnological processes by, for example, increasing the volumetric productivities of recombinant proteins or facilitating the redesign of novel biosynthetic routes for the production of metabolites. This review discusses the current applications of this technology, particularly those regarding the production of small molecules and industrially relevant recombinant enzymes. Suggestions for future research and potential uses are provided as well.

Means to optimize protein expression in transgenic plants

“…We will further clarify the importance of experimental design and highlight how new resources and design-rules can be adapted for genetic engineering. [10]. Next to a dependence on the OF tRNA abundance and the IF codon bias even altering synonymous sites on the mRNA level (maintaining the original protein sequence) can lead to tremendous effects on transcription level.…”

CodHonEditor: Spreadsheets for Codon Optimization and Editing of Protein Coding Sequences

“…It is generally recognized that several points should be considered for expression in E. coli. [1] Codon usage has been thought to be one of the most important points. Codon adaptation index, often abbreviated as CAI, is the most widely-used measure of fitness to the relative synonymous codon usage (RSCU).…”

“…However, it is widely recognized that another method of optimization, in which RSCU in the target sequence is approximated to that of the reference set, is better for maximum protein production. [1] For this purpose, codons are often randomly chosen at the probability that fit to the reference codon set, such as in OPTIMIZER. [4,5] Fitting to the reference RSCU gives only the number of each sense codon that should be present in the optimized coding sequence.…”

Recombinant protein expression in microbial systems

“…Even though IB formation is mainly regarded as a nuance in the production of recombinant proteins, Ramon and coworkers make the case that this is not always true and focus on the positive side of IBs, highlighting the advantages of producing recombinant proteins as IBs for basic and applied research (Ramon et al, 2014). No or low yield can be the result of codon bias and Elena and coauthors look into one of the strategies used for solving this problem, the expression of codon optimized genes (Elena et al, 2014). Of great importance is their account of the application of this technology in the industrial setting.…”