Abstract
Structural variations (SVs) exert important functional impacts on biological phenotypic diversity. Here we show a ring synthetic yeast chromosome V (ring_synV) can be used to continuously generate complex genomic variations and improve the production of prodeoxyviolacein (PDV) by applying Synthetic Chromosome Recombination and Modification by LoxP-mediated Evolution (SCRaMbLE) in haploid yeast cells. The SCRaMbLE of ring_synV generates aneuploid yeast strains with increased PDV productivity, and we identify aneuploid chromosome I, III, VI, XII, XIII, and ring_synV. The neochromosome of SCRaMbLEd ring_synV generated more unbalanced forms of variations, including duplication, insertions, and balanced forms of translocations and inversions than its linear form. Furthermore, of the 29 novel SVs detected, 11 prompted the PDV biosynthesis; and the deletion of uncharacterized gene YER182W is related to the improvement of the PDV. Overall, the SCRaMbLEing ring_synV embraces the evolution of the genome by modifying the chromosome number, structure, and organization, identifying targets for phenotypic comprehension.
Highlights
Structural variations (SVs) exert important functional impacts on biological phenotypic diversity
Post-SCRaMbLE, the surviving colonies with different colors could refract the fluctuation of PDV production; the color changes of surviving colonies represent the rearrangement of ring_synV
Since the synV has been demonstrated with a perfect potential to generate diverse phenotypes by SCRaMbLE, we first compared the SCRaMbLE result of ring_synV with synV by using pCre[4] plasmid[19,22]
Summary
Structural variations (SVs) exert important functional impacts on biological phenotypic diversity. We show a ring synthetic yeast chromosome V (ring_synV) can be used to continuously generate complex genomic variations and improve the production of prodeoxyviolacein (PDV) by applying Synthetic Chromosome Recombination and Modification by LoxP-mediated Evolution (SCRaMbLE) in haploid yeast cells. To continuously evolve strains of defined phenotype and genotypic SVs, we perform the inducible chromosome rearrangement by SCRaMbLEing yeast haploid cells carrying ring_synV. The ring_synV strain represents an ideal genetic background to generate inducible chromosome rearrangements while the following deletion of essential genes or occurrence of synthetic lethal genetic interactions will cause cell death; the surviving colonies could refract the fluctuation of PDV production. The SCRaMbLE method is generally useful for alteration of defined phenotype and genotype with a ring chromosome genetic background, especially for genome reorganization
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