Abstract
BackgroundThe construction of customized nucleic acid sequences allows us to have greater flexibility in gene design for recombinant protein expression. Among the various parameters considered for such DNA sequence design, individual codon usage (ICU) has been implicated as one of the most crucial factors affecting mRNA translational efficiency. However, previous works have also reported the significant influence of codon pair usage, also known as codon context (CC), on the level of protein expression.ResultsIn this study, we have developed novel computational procedures for evaluating the relative importance of optimizing ICU and CC for enhancing protein expression. By formulating appropriate mathematical expressions to quantify the ICU and CC fitness of a coding sequence, optimization procedures based on genetic algorithm were employed to maximize its ICU and/or CC fitness. Surprisingly, the in silico validation of the resultant optimized DNA sequences for Escherichia coli, Lactococcus lactis, Pichia pastoris and Saccharomyces cerevisiae suggests that CC is a more relevant design criterion than the commonly considered ICU.ConclusionsThe proposed CC optimization framework can complement and enhance the capabilities of current gene design tools, with potential applications to heterologous protein production and even vaccine development in synthetic biotechnology.
Highlights
The construction of customized nucleic acid sequences allows us to have greater flexibility in gene design for recombinant protein expression
Codon optimization formulation To investigate the relative importance of ICU and CC towards designing sequences for high protein expression, we implemented three computational procedures: the individual codon usage optimization (ICO) method generates a sequence with optimal ICU only; the codon context optimization (CCO) method optimizes sequences with regard to codon context only; and the multiobjective codon optimization (MOCO) method simultaneously considers both ICU and CC
Based on the mathematical formulation presented in Methods, the ICO problem can be described as the maximization of ICU fitness, ΨICU, subject to the constraint that the codon sequence can be translated into the target protein
Summary
The construction of customized nucleic acid sequences allows us to have greater flexibility in gene design for recombinant protein expression. In the aspect of recombinant protein production, natural genes found in wild-type organisms are usually transformed into the heterologous hosts for recombinant expression Codon usage bias has been shown to be correlated to gene expression level [7,8] As a result, this bias has been proposed as an important design parameter for enhancing recombinant protein production in heterologous expression hosts [9]. Apart from individual codon usage (ICU) bias, nonrandom utilization of adjacent codon pairs in organisms has been reported in several studies [15,16].
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