Introduction

Modulation of Selection Stringency

The directed evolution method PACE is an enormously powerful tool to improve and alter activities of different kinds of proteins for industrial, research or therapeutic applications. In some cases, a radically modified or highly specific new activity is demanded, but as a certain basal activity of the unevolved protein is necessary to propagate the selection phage (SP) with the respective accessory plasmid (AP) this task remains highly challenging. Phages encoding the unevolved protein of interest often display no or only low activity for geneIII expression on their AP. If they cannot propagate sufficiently, the phages in the lagoon are washed-out before they were able to gain favorable mutations. To decrease the stringency of an initial selection, intermediate substrates and constructs can be used as evolutionary stepping stones RN16. The difficulty consists in the fact that these evolutionary stepping stones are often not obvious or barely accessible RN46.
An easier and generally applicable approach for selection stringency modulation is a carefully regulated provision of ProteinIII independent of the favored evolving activity. This allows faint active or inactive variants to propagate in the lagoon and to accumulate mutations through evolutionary drift. Some of these mutations improve the evolving protein, which is coupled to the propagation abilities of the phages and enables phages with beneficial variants to persist higher selection pressure. The general principle of stringency modulation via controlled geneIII expression was proved by a small molecule-controlled selection stringency modulator engineered by Carlson et. al. 2014 using anhydrotetracycline (ATc) as geneIII inducer. They demonstrated that an inactive starting phage library can propagate with the addition of ATc and that a decrease of the ATc concentration leads to a selective enrichment of active mutants RN46. As exogenous chemical inducers are often limited due to transport process delay, cause toxicity or show a lack of reversibility of gene expression, we designed a novel optogenetic modulator of selection stringency CG01 CG03.

Optogenetic Tools

In the past ten years the prospects of light-regulated systems rapidly expanded and became a powerful application tool in cell biology, neuroscience, and medical research. Optogenetic tools enable the regulation of biological systems in a non-invasive and reversible manner. In contrast to widely used chemical triggers, light can be applied with high spatial and temporal precision, and does not cause unintended side effects or off-target effects, which are common for most chemical inducers. Furthermore, photosensitive proteins can be easily regulated by light intensity and duration of light illumination CG04. The naturally occuring light activated transcription factor EL222 from the marine bacterium Erythrobacter litoralis HTCC2594 consists of a N-terminal light-oxygen-voltage (LOV) domain and a C-terminal LuxR-type helix-turn-helix (HTH) motif CG04. Upon blue light irradiation with a wavelength of 450 nm, an internal flavinmononucleotide-protein adduct is formed, which results in a conformational change of the modular 222 amino acid photosensitive protein. Subsequently, a previously sequestered DNA-binding domain is exposed, which allows the homo-dimerization of EL222, and thus DNA binding. In the dark, the process spontaneously reverses. EL222 is released from the DNA, and deactivates transcription within seconds to minutesCG05.

Crystal Structure of EL222

The light-inducible transcription factor EL222 is classified into three parts: the LOV domain (blue), the conector helix (grey) and the HTH domain (red).

Motivation

The modulation of selection stringency is an essential requirement for PACE and PREDCEL based directed evolution. As we ourselves often struggled with phage wash-out during the initial selection phases, we considered the provision of a non-toxic, rapidly delivered and reversible modulator of the selection stringency as highly important for the scientific community. Our OptoSELECT systemenables an easy and prompt adaption of selection pressure to the fitness of the evolving gene pool and minimizes the experimental effort of protein optimization using PACE and PREDCEL.

Opto Select System

Design of the Opto Select System

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Increase of Phage Propagation under Blue Light using pBLind-geneIII Cassette

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