ExpressInHost: A codon tuning tool for the expression of recombinant proteins in host microorganisms

TL;DR

ExpressInHost is a user-friendly software tool that optimizes codon sequences for recombinant protein expression in host microorganisms, balancing translation speed and protein folding to improve solubility.

Contribution

It introduces a novel graphical interface with three codon tuning modes that consider host-specific tRNA resources and native codon usage.

Findings

Supports multiple tuning strategies for different expression goals

Balances translation speed and folding to reduce solubility issues

Provides an accessible tool for biotechnological applications

Abstract

ExpressInHost (https://gitlab.com/a.raguin/expressinhost) is a GTK/C++ based user friendly graphical interface that allows tuning the codon sequence of an mRNA for recombinant protein expression in a host microorganism. Heterologous gene expression is widely implemented in biotechnology companies and academic research laboratories. However, expression of recombinant proteins can be challenging. On the one hand, maximising translation speed is important, especially in scalable production processes relevant to biotechnology companies, but on the other hand, solubility problems often arise as a consequence, since translation "pauses" might be key to allow the nascent polypeptide chain to fold appropriately. To address this challenge, we have developed a software that offers three distinct modes to tune codon sequences using the genetic code redundancy. The tuning strategies implemented take into account the specific tRNA resources of the host and that of the native organism. They balance rapid translation and native speed mimicking, which might be important to allow proper protein folding, thereby avoiding protein solubility problems.