Revealing biases inherent in recombination protocols

Xiao-Song Tang,Phillip R Gibbs,Javier F Chaparro-Riggers,Karen M Polizzi,Mark J Nelson,Bernard Lw Loo,Andreas S Bommarius

doi:10.1186/1472-6750-7-77

Xiao-Song Tang, Phillip R Gibbs + Show 5 more

Open Access

https://doi.org/10.1186/1472-6750-7-77

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Abstract

BackgroundThe recombination of homologous genes is an effective protein engineering tool to evolve proteins. DNA shuffling by gene fragmentation and reassembly has dominated the literature since its first publication, but this fragmentation-based method is labor intensive. Recently, a fragmentation-free PCR based protocol has been published, termed recombination-dependent PCR, which is easy to perform. However, a detailed comparison of both methods is still missing.ResultsWe developed different test systems to compare and reveal biases from DNA shuffling and recombination-dependent PCR (RD-PCR), a StEP-like recombination protocol. An assay based on the reactivation of β-lactamase was developed to simulate the recombination of point mutations. Both protocols performed similarly here, with slight advantages for RD-PCR. However, clear differences in the performance of the recombination protocols were observed when applied to homologous genes of varying DNA identities. Most importantly, the recombination-dependent PCR showed a less pronounced bias of the crossovers in regions with high sequence identity. We discovered that template variations, including engineered terminal truncations, have significant influence on the position of the crossovers in the recombination-dependent PCR. In comparison, DNA shuffling can produce higher crossover numbers, while the recombination-dependent PCR frequently results in one crossover. Lastly, DNA shuffling and recombination-dependent PCR both produce counter-productive variants such as parental sequences and have chimeras that are over-represented in a library, respectively. Lastly, only RD-PCR yielded chimeras in the low homology situation of GFP/mRFP (45% DNA identity level).ConclusionBy comparing different recombination scenarios, this study expands on existing recombination knowledge and sheds new light on known biases, which should improve library-creation efforts. It could be shown that the recombination-dependent PCR is an easy to perform alternative to DNA shuffling.

Highlights

The recombination of homologous genes is an effective protein engineering tool to evolve proteins
The purpose of this work is to systematically compare the libraries produced by DNA shuffling and recombination-dependent PCR (RD-PCR) using the same representative templates, in order to determine the suitability of RD-PCR as a less labor-intensive alternative to DNA shuffling for the recombination of genes
One recently developed alternative to DNA shuffling is RD-PCR, which is based on simple techniques and should, in theory, produce libraries with no parental background

Summary

Introduction

The recombination of homologous genes is an effective protein engineering tool to evolve proteins. The quality of the diversity method is crucial and the performance of the chosen protocol has a direct impact on the success rate of obtaining improved variants as well as on the time and cost effectiveness of the ensuing screening or selection process [4,5]. A recent, indepth comparison of random mutagenesis methods showed that the existing methods are limited and highly biased. On average they can only achieve between 3.15–7.4 amino acid substitutions per residue [6]. DNA shuffling is the most common method with which to recombine genes, and it has become a powerful tool for protein evolution [8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23]

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