RNAi-Assisted Genome Evolution (RAGE) in Saccharomyces cerevisiae

2016 ◽  
pp. 183-198 ◽  
Author(s):  
Tong Si ◽  
Huimin Zhao
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genome Evolution

scholarly journals Rapid Colorimetric Detection of Genome Evolution in SCRaMbLEd Synthetic Saccharomyces cerevisiae Strains

2020 ◽  
Vol 8 (12) ◽  
pp. 1914
Author(s):  
Elizabeth L. I. Wightman ◽  
Heinrich Kroukamp ◽  
Isak S. Pretorius ◽  
Ian T. Paulsen ◽  
Helena K. M. Nevalainen
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genome Evolution ◽  
Colorimetric Detection ◽  
Cre Recombinase ◽  
Control Measures ◽  
Genomic Rearrangements ◽  
Industrial Yeast ◽  
Poor Growth ◽  
Yeast Strains ◽  
Industrial Strains

Genome-scale engineering and custom synthetic genomes are reshaping the next generation of industrial yeast strains. The Cre-recombinase-mediated chromosomal rearrangement mechanism of designer synthetic Saccharomyces cerevisiae chromosomes, known as SCRaMbLE, is a powerful tool which allows rapid genome evolution upon command. This system is able to generate millions of novel genomes with potential valuable phenotypes, but the excessive loss of essential genes often results in poor growth or even the death of cells with useful phenotypes. In this study we expanded the versatility of SCRaMbLE to industrial strains, and evaluated different control measures to optimize genomic rearrangement, whilst limiting cell death. To achieve this, we have developed RED (rapid evolution detection), a simple colorimetric plate-assay procedure to rapidly quantify the degree of genomic rearrangements within a post-SCRaMbLE yeast population. RED-enabled semi-synthetic strains were mated with the haploid progeny of industrial yeast strains to produce stress-tolerant heterozygous diploid strains. Analysis of these heterozygous strains with the RED-assay, genome sequencing and custom bioinformatics scripts demonstrated a correlation between RED-assay frequencies and physical genomic rearrangements. Here we show that RED is a fast and effective method to evaluate the optimal SCRaMbLE induction times of different Cre-recombinase expression systems for the development of industrial strains.

Construction of lactic acid-tolerant Saccharomyces cerevisiae by using CRISPR-Cas-mediated genome evolution for efficient d-lactic acid production

2020 ◽  
Vol 104 (21) ◽  
pp. 9147-9158
Author(s):  
Ryosuke Mitsui ◽  
Ryosuke Yamada ◽  
Takuya Matsumoto ◽  
Shizue Yoshihara ◽  
Hayato Tokumoto ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Lactic Acid ◽  
Genome Evolution ◽  
Acid Production ◽  
Lactic Acid Production ◽  
Acid Tolerant

scholarly journals Genome evolution across 1,011 Saccharomyces cerevisiae isolates

Nature ◽  
2018 ◽  
Vol 556 (7701) ◽  
pp. 339-344 ◽  
Author(s):  
Jackson Peter ◽  
Matteo De Chiara ◽  
Anne Friedrich ◽  
Jia-Xing Yue ◽  
David Pflieger ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genome Evolution

Random Base Editing for Genome Evolution in Saccharomyces cerevisiae

2021 ◽  
Author(s):  
Yingjia Pan ◽  
Siyang Xia ◽  
Chang Dong ◽  
Haojie Pan ◽  
Jin Cai ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genome Evolution ◽  
Base Editing

RNAi-Assisted Genome Evolution in Saccharomyces cerevisiae for Complex Phenotype Engineering

2014 ◽  
Vol 4 (3) ◽  
pp. 283-291 ◽  
Author(s):  
Tong Si ◽  
Yunzi Luo ◽  
Zehua Bao ◽  
Huimin Zhao
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genome Evolution ◽  
Complex Phenotype

Improved Stress Tolerance of Saccharomyces cerevisiae by CRISPR-Cas-Mediated Genome Evolution

2019 ◽  
Vol 189 (3) ◽  
pp. 810-821 ◽  
Author(s):  
Ryosuke Mitsui ◽  
Ryosuke Yamada ◽  
Hiroyasu Ogino
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Stress Tolerance ◽  
Genome Evolution

scholarly journals Loss of heterozygosity results in rapid but variable genome homogenization across genetic backgrounds in yeast

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Abhishek Dutta ◽  
Fabien Dutreux ◽  
Joseph Schacherer
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Diversity ◽  
Genome Evolution ◽  
Loss Of Heterozygosity ◽  
Genome Sequencing ◽  
Mutation Rate ◽  
Genetic Variants ◽  
Vegetative Growth ◽  
Essential Role ◽  
Large Set

The dynamics and diversity of the appearance of genetic variants play an essential role in the evolution of the genome and the shaping of biodiversity. Recent population-wide genome sequencing surveys have highlighted the importance of loss-of-heterozygosity (LOH) events and have shown that they are a neglected part of the genetic diversity landscape. To assess the extent, variability, and spectrum, we explored the accumulation of LOH events in 169 heterozygous diploid Saccharomyces cerevisiae mutation accumulation lines across nine genetic backgrounds. In total, we detected a large set of 22,828 LOH events across distinct genetic backgrounds with a heterozygous level ranging from 0.1 to 1%. LOH events are very frequent with a rate consistently much higher than the mutation rate, showing their importance for genome evolution. We observed that the interstitial LOH (I-LOH) events, resulting in internal short LOH tracts, were much frequent (n = 19,660) than the terminal LOH (T-LOH) events, i.e., tracts extending to the end of the chromosome (n = 3,168). However, the spectrum, the rate, and the fraction of the genome under LOH vary across genetic backgrounds. Interestingly, we observed that the more the ancestors were heterozygous, the more they accumulated T-LOH events. In addition, frequent short I-LOH tracts are a signature of the lines derived from hybrids with low spore fertility. Finally, we found lines showing almost complete homozygotization during vegetative progression. Overall, our results highlight that the variable dynamics of the LOH accumulation across distinct genetic backgrounds might lead to rapid differential genome evolution during vegetative growth.

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