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Engineering Global Transcription to Tune Lipophilic Properties in Yarrowia Lipolytica

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Engineering Global Transcription to Tune Lipophilic Properties in Yarrowia Lipolytica Wang et al. Biotechnol Biofuels (2018) 11:115 https://doi.org/10.1186/s13068-018-1114-z Biotechnology for Biofuels RESEARCH Open Access Engineering global transcription to tune lipophilic properties in Yarrowia lipolytica Man Wang1,2†, Guan‑Nan Liu3†, Hong Liu1,2, Lu Zhang1,2, Bing‑Zhi Li1,2, Xia Li1,2, Duo Liu1,2* and Ying‑Jin Yuan1,2 Abstract Background: Evolution of complex phenotypes in cells requires simultaneously tuning expression of large amounts of genes, which can be achieved by reprograming global transcription. Lipophilicity is an important complex trait in oleaginous yeast Yarrowia lipolytica. It is necessary to explore the changes of which genes’ expression levels will tune cellular lipophilic properties via the strategy of global transcription engineering. Results: We achieved a strategy of global transcription engineering in Y. lipolytica by modifying the sequences of a key transcriptional factor (TF), SPT15-like (Yl-SPT15). The combinatorial mutagenesis of this gene was achieved by DNA assembly of up to fve expression cassettes of its error-prone PCR libraries. A heterologous beta-carotene biosynthetic pathway was constructed to research the efects of combined Yl-SPT15 mutants on carotene and lipid production. As a result, we obtained both an “enhanced” strain with 4.7-fold carotene production and a “weakened” strain with 0.13- fold carotene production relative to the initial strain, nearly 40-fold changing range. Genotype verifcation, compara‑ tive transcriptome analysis, and detection of the amounts of total and free fatty acids were made for the selected strains, indicating efective tuning of cells’ lipophilic properties. We exploited the key pathways including RNA polymerase, ketone body metabolism, fatty acid synthesis, and degradation that drastically determined cells’ variable lipophilicity. Conclusions: We have examined the efects of combinatorial mutagenesis of Yl-SPT15 on cells’ capacity of producing beta-carotene and lipids. The lipophilic properties in Y. lipolytica could be efectively tuned by simultaneously regulat‑ ing genome-wide multi-gene expression levels. The exploited gene targets and pathways could guide design and reconstruction of yeast cells for tunable and optimal production of other lipophilic products. Keywords: Yarrowia lipolytica, Global transcription engineering, DNA assembly, Transcription factor, Beta-carotene, Fatty acid, Lipid Background why and how cells choose and accept special changes to Metabolic engineering and synthetic biology has devel- meet target functions. An accessible strategy is global oped versatile tools to engineer certain metabolic path- transcriptional machinery engineering (gTME), which ways to get optimal product synthesis and hyperburst was frstly reported by Stephanopoulos’ group [6, 7]. of target functions [1–5]. However, evolution of com- Gene sequences of transcription factors are subjected plex traits in cells always demands arranging the expres- to mutation via error-prone polymerase chain reac- sion levels of larger range of genes. If we can construct a tion (PCR) or site-directed mutagenesis methods, lead- wide change of gene expression, we can also understand ing to changeable promotor preferences and efciency of RNA polymerase, which further modulates genome- wide transcription levels to varied extents. Te diver- *Correspondence: [email protected] sity of changed transcriptomes confers diverse probable †Man Wang and Guan-Nan Liu contributed equally to this work phenotypes on cells [6–12]. Tis strategy has already 1 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, been used in several organisms, such as Escherichia Tianjin 300072, People’s Republic of China coli, Saccharomyces cerevisiae, and Zymomonas mobilis, Full list of author information is available at the end of the article © The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/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://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Wang et al. Biotechnol Biofuels (2018) 11:115 Page 2 of 15 ofering efective methods to generate novel mutants of Spt15 resulted in pleiotropic changes of gene tran- with enhanced environmental tolerance, metabolite pro- scription levels [32, 33]. Te SPT15 gene mutants were duction, and substrate utilization [6–8, 11, 12]. Besides, demonstrated feasibility to phenotypic evolution in S. several transcription factors have been successfully engi- cerevisiae in many ways, such as enhancing ethanol pro- neered to optimize performance of strains, such as sigma duction [34], improving xylose fermentation [10], and factor, CRP, Spt15, H-NS, and Hha [10, 13–15]. In oleagi- enhancing adaptation to corn cob acid hydrolysate [11]. nous yeast Yarrowia lipolytica, a similar strategy of global For modifying Yl-Spt15 (a potential TF) in Y. lipolytica, transcription engineering is in demand to tune cellular we constructed combinatorial mutagenesis of its cod- complex phenotypes such as lipophilicity which usually ing gene and screened the optimal mutant combinations requires participation of large amounts of genes. for enhanced production of beta-carotene, which was In recent years, Y. lipolytica attracts more attention as synthesized as a non-native product by a heterologous this yeast produces high-level lipids and its gene manipu- pathway (Fig. 1). A 40-fold changing range of carotene lation is available [16–19]. Metabolic pathway engineering production was obtained and the further analysis of the has been used to improve production of several valuable selected strains indicated efective tuning of lipophilic products such as biofuels, polyunsaturated fatty acids, properties. We exploited the key changed pathways and and carotenoids [20–25]. Te experience obtained from ofered guidance for tuning yeast lipophilicity to produce rational engineering of model organism E. coli and S. cer- other high value-added lipophilic products. evisiae has also been proved efective in Y. lipolytica, for example, for carotenoid synthesis. Wu et al. [26] improved Results the production of beta-carotene in E. coli to 44.2 mg/g Expression of Yl‑SPT15 mutant libraries in assembled DCW in fasks by combining strategies of modular path- cassettes way engineering and membrane engineering. Xie et al. According to the amino acid sequence of Spt15 in S. cer- [27] constructed a S. cerevisiae strain producing 1.156 g/L evisiae, we searched the conserved domains in Y. lipol- (20.79 mg/g DCW) of carotenoids using sequential con- ytica by BLAST in NCBI database and got a Spt15-like trol strategy in fermentation. Chen et al. [28] got 1.65 g/L protein named as Yl-Spt15 coded by YALIOB23056g (55.56 mg/g DCW) of lycopene from fermentation of S. on chromosome B (Fig. 1a and Additional fle 1: Figure cerevisiae by combining chassis engineering and heterolo- S1). Tis Yl-Spt15 owned the same conserved regions gous pathway engineering. As for Y. lipolytica, the native of “repeat element 1,” “helix 2,” “repeat element 2,” and tHMGR and ERG series genes were overexpressed in Gao’s “helix 2’” with Spt15 (Additional fle 1: Figure S1, Addi- work to improve fermentative production of beta-carotene tional fle 2). Since the mutants of Spt15 in S. cerevisiae to 4 g/L [23]. A recent work reported that the strain highly were proved efective to promote phenotypic evolution accumulating lipids could also highly produce carotenoids in many ways, we decided to construct the mutants of its [29]. Tey achieved a fermentative production of beta- potential counterpart Yl-Spt15 in Y. lipolytica to test its carotene of 6.5 g/L (90 mg/g DCW) with a concomitant efects on product synthesis such as lipophilic products production of 42.6 g/L of lipids. However, the deep tuning [10, 11, 34]. Te manipulated Yl-SPT15 mutant libraries mode of competitive synthesis of fatty acids, lipids, and (see “Methods” for detailed construction process) were other heterologous lipophilic products like carotenoids inserted in designed fve expression cassettes and assem- was not clearly elucidated. Some distant pathway enzymes bled meanwhile integrated in yeast chromosomal GUT2 such as transporters and coenzymes could also tune lipid site by in vivo homologous recombination (HR) (Fig. 1b, product synthesis [21, 30]. It was necessary to research Additional fle 1: Figure S2a, b and “Methods”). Te cor- how Y. lipolytica tunes its gene expression to afect internal rect rate of three-cassette assembly and integration at lipophilicity to gain appropriate levels of native lipids and GUT2 site was about 7.3% and could be further improved heterologous lipophilic products. to 18.0% in the strain with ku70 knockout (Additional Here we report a strategy of engineering global tran- fle 1: Figure S3). Although the efciency was not so high, scription in Y. lipolytica to tune the complex lipophilic- this site primarily could be employed for integration of ity and detailed lipophilic properties such as carotenoids, multiple Yl-SPT15 mutants. Tis kind of combinatorial fatty acids and lipid bodies. In eukaryote’s
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