Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites

• Published in: PLoS computational biology Vol. 17; no. 10; p. e1009461
• Main Authors: Bhandari, Bikash K, Lim, Chun Shen, Remus, Daniela M, Chen, Augustine, van Dolleweerd, Craig, Gardner, Paul P
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01-10-2021; Public Library of Science (PLoS)
• Subjects: Accessibility; Biology and Life Sciences; Biosynthesis; Codon; Codon, Initiator - genetics; Codon, Terminator - genetics; Codons; Computational Biology; Datasets; E coli; Energy; Experiments; Genetic translation; Libraries; Medical research; Methods; mRNA; Pharmaceutical industry; Physical Sciences; Physiological aspects; Production processes; Protein expression; Proteins; Recombinant proteins; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Research and Analysis Methods; Silent Mutation - genetics; Simulated annealing; Species diversity; Stochasticity; Transfer RNA; Translation; Translation initiation; New Zealand
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1009461

Recombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. Here we show that the accessibility of translation initiation sites modelled using the mRNA base-unpairing across the Boltzmann's ensemble significantly outperforms alternative features. This approach accurately predicts the successes or failures of expression experiments, which utilised Escherichia coli cells to express 11,430 recombinant proteins from over 189 diverse species. On this basis, we develop TIsigner that uses simulated annealing to modify up to the first nine codons of mRNAs with synonymous substitutions. We show that accessibility captures the key propensity beyond the target region (initiation sites in this case), as a modest number of synonymous changes is sufficient to tune the recombinant protein expression levels. We build a stochastic simulation model and show that higher accessibility leads to higher protein production and slower cell growth, supporting the idea of protein cost, where cell growth is constrained by protein circuits during overexpression.