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Scramble Generates Evolved Yeasts with Increased Alkali Tolerance Lu Ma1,2, Yunxiang Li1,2, Xinyu Chen1,2, Mingzhu Ding1,2, Yi Wu1,2* and Ying‑Jin Yuan1,2

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Scramble Generates Evolved Yeasts with Increased Alkali Tolerance Lu Ma1,2, Yunxiang Li1,2, Xinyu Chen1,2, Mingzhu Ding1,2, Yi Wu1,2* and Ying‑Jin Yuan1,2 Ma et al. Microb Cell Fact (2019) 18:52 https://doi.org/10.1186/s12934-019-1102-4 Microbial Cell Factories RESEARCH Open Access SCRaMbLE generates evolved yeasts with increased alkali tolerance Lu Ma1,2, Yunxiang Li1,2, Xinyu Chen1,2, Mingzhu Ding1,2, Yi Wu1,2* and Ying‑Jin Yuan1,2 Abstract Background: Strains with increased alkali tolerance have a broad application in industrial, especially for bioremedia‑ tion, biodegradation, biocontrol and production of bio‑based chemicals. A novel synthetic chromosome recombina‑ tion and modifcation by LoxP‑mediated evolution (SCRaMbLE) system has been introduced in the synthetic yeast genome (Sc 2.0), which enables generation of a yeast library with massive structural variations and potentially drives phenotypic evolution. The structural variations including deletion, inversion and duplication have been detected within synthetic yeast chromosomes. Results: Haploid yeast strains harboring either one (synV) or two (synV and synX) synthetic chromosomes were subjected to SCRaMbLE. Seven of evolved strains with increased alkali tolerance at pH 8.0 were generated through multiple independent SCRaMbLE experiments. Various of structural variations were detected in evolved yeast strains by PCRTag analysis and whole genome sequencing including two complex structural variations. One possessed an inversion of 20,743 base pairs within which YEL060C (PRB1) was deleted simultaneously, while another contained a duplication region of 9091 base pairs in length with a deletion aside. Moreover, a common deletion region with length of 11,448 base pairs was mapped in four of the alkali‑tolerant strains. We further validated that the deletion of YER161C (SPT2) within the deleted region could increase alkali tolerance in Saccharomyces cerevisiae. Conclusions: SCRaMbLE system provides a simple and efcient way to generate evolved yeast strains with enhanced alkali tolerance. Deletion of YER161C (SPT2) mapped by SCRaMbLE can improve alkali tolerance in S. cerevisiae. This study enriches our understanding of alkali tolerance in yeast and provides a standard workfow for the application of SCRaMbLE system to generate various phenotypes that may be interesting for industry and extend understanding of phenotype‑genotype relationship. Keywords: SCRaMbLE, Alkali tolerance, Synthetic biology, Saccharomyces cerevisiae, SPT2 Background engineer biological systems. Traditional techniques such Genomic variation drives phenotypic diversifcation in as physical and chemical mutagenesis and error-prone populations and evolutionary changes among diferent PCR, could generate mutations in vivo and in vitro at the species [1–3]. Genome evolution in nature is a long-term level of single nucleotide polymorphisms or insertion- process with accumulation of DNA variation that mainly deletion [7, 8]. Genome-editing technique mediated by involves single nucleotide polymorphisms (SNP), inser- TALEN, ZFN or CRISPR-Cas9 has made it possible to tion-deletion (InDel) and structural variation (SV) [4–6]. edit one or multiple targets on the genome rationally and Accordingly, techniques of manipulating varied length precisely [9–11]. However, very few techniques related to of DNA are constantly being developed and updated to large-scale genome rearrangement are reported to gen- erate a structural variation library. Te synthetic yeast genome project (Sc 2.0 project) is designed to encode an *Correspondence: [email protected] inducible genome rearrangement system in the chemi- 1 Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, cally synthesized yeast genome by thousands of loxP- Tianjin 300072, China sym sites inserted in the 3′ untranslated region (UTR) of Full list of author information is available at the end of the article nonessential genes [12–18]. With the expression of Cre © The Author(s) 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat iveco mmons .org/licen ses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/ publi cdoma in/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Ma et al. Microb Cell Fact (2019) 18:52 Page 2 of 11 recombinase in vivo, the synthetic chromosome recom- chromosomes were subjected to SCRaMbLE in this bination and modifcation by LoxP-mediated evolution study. Cre recombinase fused with estrogen-binding (SCRaMbLE) system could drive generation of a yeast domain (EBD) has been used to control the SCRaM- library with massive structural variations. Te structural bLE system in previous studies [19, 22]. Two Cre-EBD variations including deletion, inversion and duplication plasmids pYW079 (pRS416-pSCW11-Cre-EBD) and have been detected within synthetic yeast chromosomes pYW180 (pRS416-pCLB2-Cre-EBD) with diferent pro- and ring synthetic yeast chromosomes after SCRaMbLE- moters were transformed to strains yXZX846 (synV) and ing [19, 20]. Moreover, some evolved yeast strains with yYW169 (synV&X). pCLB2 is a G2/M-specifc promoter enhanced phenotype (i.e., temperature tolerance, cafeine which could lead cells to expose to Cre recombinase con- tolerance, production of carotenoids) have been gener- tinually in each cell cycle [34], while pSCW11 is a strong ated by SCRaMbLE system, showing promising applica- promoter which only initiates transcription in daughter tion of this technology [21–27]. cells [35]. β-Estradiol was added in medium to enable the Extracellular pH, as an important environmental con- fusion protein Cre-EBD to transfer into cell nucleus and dition, has a signifcant infuence on the survival and bind to the loxPsym sites in the synthetic chromosomes, growth of cells. As a model organism, S. cerevisiae grows resulting an activated SCRaMbLE system. more rapidly in acidic than neutral or alkaline pH [28, Although the loxPsym sites were inserted in the 3′ 29]. It is important to study this underling mechanism UTR of non-essential genes, essential genes might be for the application of industrial fermentation in alkaline deleted by Cre/loxPsym reaction across these genes, environments. Te discoveries of genes related to alkali resulting the loss of viability for haploid synthetic yeasts. tolerance in previous studies have been reported via ran- We characterized the lethality caused by SCRaMbLE dom mutation, long-term adaptive evolution, deletion frstly. As shown in Fig. 2a, lethality of strains carry- or overexpression of a dubious gene [29–32]. Te tran- ing pYW079 was higher than strains carrying pYW180 scriptional response to alkaline stress in S. cerevisiae was due to the enhanced expression of Cre recombinase by also studied by a short-term exposure in alkaline pH [33]. a stronger promoter. And lethality of synV&X strains However, these methods are non-rational designed and was slightly higher than synV strain. Tis may be caused make it complicated to uncover phenotype-genotype by larger number of loxPsym sites within two synthetic correlations. In this study, we accelerated the evolution chromosomes in synV&X strains. After 8 h’ SCRaMbLE, of synthetic yeast strains in alkaline pH using SCRaMbLE more than 70% lethality was detected in strains carried system. Two synthetic yeast strains synV and synV&X, pYW180 and more than 90% lethality in strains carried which harbor one synthetic yeast chromosome V and pYW079. Ten 8 h’ SCRaMbLE was considered as an two synthetic yeast chromosomes V and X respectively, appropriate intensity of genome evolution and chosen for were used as initial strains [12, 13]. Trough multiple the following SCRaMbLE experiments. independent SCRaMbLE experiments, seven of evolved strains with increased alkali tolerance at pH 8.0 were SCRaMbLE generates evolved yeasts with increased alkali obtained. Many structural variations were detected in tolerance the evolved yeast strains by PCRTag analysis and whole YPD media with diferent pH were tested to select an genome sequencing. A common deletion region with appropriate alkaline condition for screening of SCRaM- length of 11,448 base pairs has been mapped in four of bLEd strains. pH 8.0 was chosen as the selective condi- the alkali-tolerant strains. We further validated that the tion as showing enough alkaline pressure while keeping deletion of YER161C (SPT2) in this region could lead a reasonable culture time. Several bigger colonies from to the enhanced phenotype under alkaline stress. Te the SCRaMbLEd pool were detected though visual SCRaMbLE method provides an efcient way to gener- inspection on the selective plates after cultured at 30 °C ate evolved strains with increased alkali tolerance and a for 4 days, while very few big colonies were grown on straightforward way to dissect the correlation of pheno- the selective plates from unSCRaMbLE pool (Fig. 2b). type and genotype (Fig. 1). To avoid the possible leaky expression of Cre recombi- nase on candidate strains, the Cre-EBD plasmids were Results and discussion lost via serially culturing in YPD liquid medium. A total Construction and characterization of SCRaMbLE system of seven strains (yML008, yML011, yML013, yML015, Synthetic yeast chromosome V (synV) is 536,024 base yML098, yML099 and yML110) generated through
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