Ring synthetic chromosome V SCRaMbLE

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.

Engineering yeast artificial core promoter with designated base motifs

“…From another angle, we need this kind of de novo designed artificial promoters as barcodes to mark gene expression at genome level to research the genome rearrangement [18,19]. The artificial barcodes of promoters will further assist the analysis of synthetic genomic evolution.…”

Chromosome drives via CRISPR-Cas9 in yeast

“…As part of the Sc2.0 project, synthetic yeast chromosomes have been designed with hundreds of palindromic loxPsym sites located downstream of nonessential genes throughout the chromosomes 25,26 . Genomic segments between loxPsym sites can be rearranged with the expression of Cre recombinase, which leads to stochastic deletion, inversion, translocation, and duplication within and between synthetic chromosomes, which is referred to as the Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system [37][38][39][40] . Under suitable screening conditions, SCRaMbLEd strains with improved traits can be generated 38,40 .…”

“…Genomic segments between loxPsym sites can be rearranged with the expression of Cre recombinase, which leads to stochastic deletion, inversion, translocation, and duplication within and between synthetic chromosomes, which is referred to as the Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system [37][38][39][40] . Under suitable screening conditions, SCRaMbLEd strains with improved traits can be generated 38,40 . However, owing to the process of totally random chromosomal rearrangement, it is still a challenge to dissect the structural variations that lead to specific phenotypic changes [38][39][40] .…”

“…Under suitable screening conditions, SCRaMbLEd strains with improved traits can be generated 38,40 . However, owing to the process of totally random chromosomal rearrangement, it is still a challenge to dissect the structural variations that lead to specific phenotypic changes [38][39][40] . Here, we used chromosome drive to attempt to transmit the newly generated unresolved trait of chromium resistance.…”

Improved betulinic acid biosynthesis using synthetic yeast chromosome recombination and semi-automated rapid LC-MS screening

“…In previous works, synthetic chromosomes have been SCRaMbLEd and yeast strains selected with improved tolerance to either high alkali conditions 15 , caffeine 16 , heat 16,17 , ethanol 17 , or acetic acid 17 . SCRaMbLE has also been used to improve the performance of yeast strains in biosynthesis of heterologous metabolites, including strains engineered with pathways for violacein 16,18,19 and for carotene and lycopene 16,20,21 .…”