Improving prodeoxyviolacein production via multiplex SCRaMbLE iterative cycles
Juan Wang1,2, Bin Jia1,2, Zexiong Xie1,2, Yunxiang Li1,2, Yingjin Yuan1,2()
1. Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China 2. SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
The synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) system has been used to improve prodeoxyviolacein (PDV) production in haploid yeast containing chromosome synV. To rapidly and continuously generate genome diversification with the desired phenotype, the multiplex SCRaMbLE iterative cycle strategy has been developed for the screening of high PDV production strains. Whole-genome sequencing analysis reveals large duplications, deletions, and even the whole genome duplications. The deletion of YER151C is proved to be responsible for the increase. This study demonstrates that artificial DNA rearrangement can be used to accelerate microbial evolution and the production of biobased chemicals.
J SDymond, S M Richardson, C E Coombes, T Babatz, HMuller, NAnnaluru, W JBlake, J WSchwerzmann, J BDai, D LLindstrom, et al. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature, 2011, 477(7365): 471–476 https://doi.org/10.1038/nature10403
2
J XYue, J Li, LAigrain, JHallin, KPersson, KOliver, ABergström, PCoupland, JWarringer, M CLagomarsino, et al. Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nature Genetics, 2017, 49(6): 913–924 https://doi.org/10.1038/ng.3847
3
Q JZhang, T Zhu, E HXia, CShi, Y L Liu, Y Zhang, YLiu, W KJiang, Y JZhao, S YMao, et al. Rapid diversification of five Oryza AA genomes associated with rice adaptation. Nucleic Acids Research, 2014, 111(46): e4954–e4962
4
PPevzner, G Tesler. Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes. Genome Research, 2003, 13(1): 37–45 https://doi.org/10.1101/gr.757503
5
RRedon, S Ishikawa, K RFitch, LFeuk, H George, T DAndrews, HFiegler, M HShapero, A RCarson, W WChen, et al. Global variation in copy number in the human genome. Nature, 2006, 444(7118): 444–454 https://doi.org/10.1038/nature05329
6
Y XZhang, K Perry, V AVinci, KPowell, W P CStemmer, S BDel Cardayré. Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature, 2002, 415(6872): 644–646 https://doi.org/10.1038/415644a
7
DBiot-Pelletier, V J J Martin. Evolutionary engineering by genome shuffling. Applied Microbiology and Biotechnology, 2014, 98(9): 3877–3887 https://doi.org/10.1007/s00253-014-5616-8
8
Z XXie, B Z Li, L A Mitchell, Y Wu, XQi, ZJin, B Jia, XWang, B XZeng, H MLiu, et al. “Perfect” designer chromosome V and behavior of a ring derivative. Science, 2017, 355(6329): 1046
9
YWu, B Z Li, M Zhao, L AMitchell, Z XXie, Q HLin, XWang, W H Xiao, Y Wang, XZhou, et al. Bug mapping and fitness testing of chemically synthesized chromosome X. Science, 2017, 355(6329): 1048
10
NDurán, G Z Justo, M Durán, MBrocchi, LCordi, LTasic, G RCastro, GNakazato. Advances in chromobacterium violaceum and properties of violacein–its main secondary metabolite: A review. Biotechnology Advances, 2016, 34(5): 1030–1045 https://doi.org/10.1016/j.biotechadv.2016.06.003
MKonzen, D De Marco, C A SCordova, T OVieira, R VAntônio, T BCreczynski-Pasa. Antioxidant properties of violacein: Possible relation on its biological function. Bioorganic & Medicinal Chemistry, 2006, 14(24): 8307–8313 https://doi.org/10.1016/j.bmc.2006.09.013
13
NDurán, R V Antonio, M Haun, R APilli. Biosynthesis of a trypanocide by Chromobacterium violaceum. World Journal of Microbiology & Biotechnology, 1994, 10(6): 686–690 https://doi.org/10.1007/BF00327960
14
PAntonisamy, S Ignacimuthu. Immunomodulatory, analgesic and antipyretic effects of violacein isolated from Chromobacterium violaceum. Phytomedicine, 2010, 17(3–4): 300–304 https://doi.org/10.1016/j.phymed.2009.05.018
15
M ELee, A Aswani, A SHan, C JTomlin, J EDueber. Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay. Nucleic Acids Research, 2013, 41(22): 10668–10678 https://doi.org/10.1093/nar/gkt809
16
QLin, B Jia, L AMitchell, J CLuo, KYang, K I Zeller, W Q Zhang, Z W Xu, G Stracquadanio, J SBader, J DBoeke, Y JYuan. RADOM, an Efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae. ACS Synthetic Biology, 2014, 4(3): 213–220 https://doi.org/10.1021/sb500241e
17
DLiu, H Liu, B ZLi, HQi, B Jia, XZhou, H XDu, WZhang, Y JYuan. Multigene pathway engineering with regulatory linkers (M-PERL). ACS Synthetic Biology, 2016, 5(12): 1535–1545 https://doi.org/10.1021/acssynbio.6b00123
18
A RKnaggs. The biosynthesis of shikimate metabolites. Natural Product Reports, 2003, 20(1): 119–136 https://doi.org/10.1039/b100399m
19
J GZalatan, M Lee, E RAlmeida, L AGilbert, E HWhitehead, MLa Russa, J CTsai, J SWeissman, J EDueber, L SQi, W ALim. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell, 2015, 160(1–2): 339–350 https://doi.org/10.1016/j.cell.2014.11.052
20
BJia, Y Wu, B ZLi, L AMitchell, HLiu, S Pan, JWang, H RZhang, H MLiu, Z XChen, et al. Precise control of SCRaMbLE in synthetic haploid and diploid yeast. Nature Communications, 2018, 9(1): 1933 https://doi.org/10.1038/s41467-018-03084-4
21
AQuerol, M T Fernández-Espinar, M Del Olmo, EBarrio. Adaptive evolution of wine yeast. International Journal of Food Microbiology, 2003, 86(1–2): 3–10 https://doi.org/10.1016/S0168-1605(03)00244-7
22
LGatti, K L Hoe, J Hayles, S CRighetti, N BCarenini, DLaura, D UKim, H OPark, PPerego. Ubiquitin-proteasome genes as targets for modulation of cisplatin sensitivity in fission yeast. BMC Genomics, 2011, 12(1): 44 https://doi.org/10.1186/1471-2164-12-44
23
S EDodgson, S Santaguida, SKim, JSheltzer, AAmon. The pleiotropic deubiquitinase UBP3 confers aneuploidy tolerance. Genes & Development, 2016, 30(20): 2259–2271 https://doi.org/10.1101/gad.287474.116
24
DLiu, B Z Li, H Liu, X JGuo, Y JYuan. Profiling influences of gene overexpression on heterologous resveratrol production in Saccharomyces cerevisiae. Frontiers of Chemical Science and Engineering, 2017, 11(1): 117–125 https://doi.org/10.1007/s11705-016-1601-3
25
R ZWang, X L Gu, M D Yao, C H Pan, H Liu, W HXiao, YWang, Y J Yuan. Engineering of β-carotene hydroxylase and ketolase for astaxanthin overproduction in Saccharomyces cerevisiae. Frontiers of Chemical Science and Engineering, 2017, 11(1): 89–99 https://doi.org/10.1007/s11705-017-1628-0
26
Y JYuan, J C Wu, X Wang. Collaborations of China with the world in Synbio. Frontiers of Chemical Science and Engineering, 2017, 11(1): 1–2 https://doi.org/10.1007/s11705-017-1638-y
