Directed yeast genome evolution by controlled introduction of trans-chromosomic structural variations

Area of Science:

• Genomics
• Synthetic Biology
• Biotechnology

Background:

• Structural variations (SVs) significantly contribute to genomic diversity and influence chromosome 3D architecture.
• Developing controllable methods to engineer complex SVs and understand their mechanisms has been challenging.

Purpose of the Study:

• To develop a method for controlled induction of complex SVs using Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE).
• To demonstrate the application of engineered SVs in enhancing the biosynthesis of valuable compounds like astaxanthin.

Main Methods:

• Creation of an SV-prone yeast strain utilizing two synthetic chromosomes (synV and synX) with SCRaMbLE technology.
• Rational design and induction of specific SVs, including pericentric inversion and trans-chromosome translocation.
• Using astaxanthin biosynthesis as a readout to quantify the impact of SVs on yield.

Main Results:

• Engineered yeast with complex SVs, including two neo-chromosomes, exhibited a 2.7-fold increase in astaxanthin yield.
• Identified genetic targets associated with increased astaxanthin production, confirming SVs' role in reorganizing genetic information.
• Successfully demonstrated precise induction of trans-chromosome translocations and pericentric inversions.

Conclusions:

• SCRaMbLE technology provides an effective tool for directed genome evolution and understanding SV mechanisms.
• Engineered SVs can be rationally designed to alter phenotypes, such as enhancing the production of industrially relevant compounds.