Methods for measuring the evolutionary stability of engineered genomes to improve their longevity

Area of Science:

• Microbial Engineering
• Evolutionary Biology
• Synthetic Biology

Background:

• Engineered microbes often carry foreign transgenes that provide no benefit to the host.
• This 'engineered baggage' is subject to rapid evolutionary loss during microbial propagation.
• Maintaining transgenes long-term is critical for many biotechnological applications.

Purpose of the Study:

• To develop a method for jointly estimating the mutation rate of transgene loss and the strength of selection favoring transgene-free revertants.
• To provide tools for predicting the evolutionary half-life of engineered transgenes.
• To quantify the impact of altering mutation rates and selection strength on transgene longevity.

Main Methods:

• Utilizing data from serial transfer experiments where engineered genome frequency is monitored.
• Developing simple mathematical models to estimate mutation rates and selection strength.
• Implementing the estimation and prediction tools in an interactive web application (MuSe).

Main Results:

• A method for jointly estimating transgene loss mutation rate and selection strength was established.
• Mathematical models were developed to predict transgene evolutionary half-life.
• Quantitative predictions for the influence of mutation and selection on transgene longevity were generated.

Conclusions:

• The developed method and tools enable better prediction of transgene stability in engineered microbes.
• Understanding and quantifying evolutionary pressures are key to enhancing the longevity of engineered genetic elements.
• The MuSe web application provides a practical resource for researchers in microbial engineering and synthetic biology.