Rapid evolution of recombinant Saccharomyces cerevisiae for Xylose fermentation through formation of extra-chromosomal circular DNA

PLoS Genetics
Mekonnen M DemekeJohan M Thevelein

Abstract

Circular DNA elements are involved in genome plasticity, particularly of tandem repeats. However, amplifications of DNA segments in Saccharomyces cerevisiae reported so far involve pre-existing repetitive sequences such as ribosomal DNA, Ty elements and Long Terminal Repeats (LTRs). Here, we report the generation of an eccDNA, (extrachromosomal circular DNA element) in a region without any repetitive sequences during an adaptive evolution experiment. We performed whole genome sequence comparison between an efficient D-xylose fermenting yeast strain developed by metabolic and evolutionary engineering, and its parent industrial strain. We found that the heterologous gene XylA that had been inserted close to an ARS sequence in the parent strain has been amplified about 9 fold in both alleles of the chromosomal locus of the evolved strain compared to its parent. Analysis of the amplification process during the adaptive evolution revealed formation of a XylA-carrying eccDNA, pXI2-6, followed by chromosomal integration in tandem arrays over the course of the evolutionary adaptation. Formation of the eccDNA occurred in the absence of any repetitive DNA elements, probably using a micro-homology sequence of 8 nucleotides flanking the am...Continue Reading

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Citations

Sep 18, 2015·Journal of Industrial Microbiology & Biotechnology·Vratislav StovicekIrina Borodina
Jun 26, 2015·Yeast·Uroš Petrovič
Apr 1, 2017·Biotechnology for Biofuels·David PerisChris Todd Hittinger
Dec 22, 2016·Scientific Reports·Leandro Vieira Dos SantosGonçalo Amarante Guimarães Pereira
Mar 2, 2016·International Journal of Molecular Sciences·Danuza Nogueira MoysésFernando Araripe Gonçalves Torres
Mar 16, 2018·Nature Communications·Henrik Devitt MøllerBirgitte Regenberg
Jul 10, 2019·Future Science OA·Ishita TandonNilesh K Sharma
Dec 4, 2019·PLoS Biology·Ryan M HullJonathan Houseley
Jun 28, 2018·Applied Microbiology and Biotechnology·Xinyuan ZhangLimin Cao
Apr 17, 2020·Current Genetics·Ryan M Hull, Jonathan Houseley

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Datasets Mentioned

BETA
SRX651886
SRX647780

Methods Mentioned

BETA
PCR
electrophoresis
Illumina sequencing

Software Mentioned

GraphPad prism
CLC Genomics Workbench5

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