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© Melanie Blokesch, EPFL
Flagellated Vibrio cholerae
Publication : Biotechnology & Bioengineering

Recoding of synonymous genes to expand evolutionary landscapes requires control of secondary structure affecting translation

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Biotechnology & Bioengineering - 17 Oct 2017

Escudero JA, Nivina A, Cambray G, López-Igual R, Loot C, and Mazel D.

Link to Pubmed [PMID] – 28898391

Biotechnology & Bioengineering (2018) 115(1):184-191. doi: 10.1002/bit.26450

Synthetic DNA design needs to harness the many information layers embedded in a DNA string. We previously developed the Evolutionary Landscape Painter (ELP), an algorithm that exploits the degeneracy of the code to increase protein evolvability. Here, we have used ELP to recode the integron integrase gene (intI1) in two alternative alleles. Although synonymous, both alleles yielded less IntI1 protein and were less active in recombination assays than intI1. We spliced the three alleles and mapped the activity decrease to the beginning of alternative sequences. Mfold predicted the presence of more stable secondary structures in the alternative genes. Using synonymous mutations, we decreased their stability and recovered full activity. Following a design-build-test approach, we have now updated ELP to consider such structures and provide streamlined alternative sequences. Our results support the possibility of modulating gene activity through the ad hoc design of 5′ secondary structures in synthetic genes.

http://onlinelibrary.wiley.com/doi/10.1002/bit.26450/abstract;jsessionid=2ECF14AD1B1592296E9440AF64F9C41D.f03t03