Improving prodeoxyviolacein production via multiplex SCRaMbLE iterative cycles

Abstract

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.

Graphical abstract

Keywords

synthetic biology / genome rearrangement / prodeoxyviolacein / SCRaMbLE / Saccharomyces cerevisiae

References

[1] Dymond J S, Richardson S M, Coombes C E, Babatz T, Muller H, Annaluru N, Blake W J, Schwerzmann J W, Dai J B, Lindstrom D L, Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature, 2011, 477(7365): 471–476

[2] Yue J X, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Lagomarsino M C, Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nature Genetics, 2017, 49(6): 913–924

[3] Zhang Q J, Zhu T, Xia E H, Shi C, Liu Y L, Zhang Y, Liu Y, Jiang W K, Zhao Y J, Mao S Y, Rapid diversification of five Oryza AA genomes associated with rice adaptation. Nucleic Acids Research, 2014, 111(46): e4954–e4962

[4] Pevzner P, Tesler G. Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes. Genome Research, 2003, 13(1): 37–45

[5] Redon R, Ishikawa S, Fitch K R, Feuk L, George H, Andrews T D, Fiegler H, Shapero M H, Carson A R, Chen W W, Global variation in copy number in the human genome. Nature, 2006, 444(7118): 444–454

[6] Zhang Y X, Perry K, Vinci V A, Powell K, Stemmer W P C, Del Cardayré S B. Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature, 2002, 415(6872): 644–646

[7] Biot-Pelletier D, Martin V J J. Evolutionary engineering by genome shuffling. Applied Microbiology and Biotechnology, 2014, 98(9): 3877–3887

[8] Xie Z X, Li B Z, Mitchell L A, Wu Y, Qi X, Jin Z, Jia B, Wang X, Zeng B X, Liu H M, “Perfect” designer chromosome V and behavior of a ring derivative. Science, 2017, 355(6329): 1046

[9] Wu Y, Li B Z, Zhao M, Mitchell L A, Xie Z X, Lin Q H, Wang X, Xiao W H, Wang Y, Zhou X, Bug mapping and fitness testing of chemically synthesized chromosome X. Science, 2017, 355(6329): 1048

[10] Durán N, Justo G Z, Durán M, Brocchi M, Cordi L, Tasic L, Castro G R, Nakazato G. Advances in chromobacterium violaceum and properties of violacein–its main secondary metabolite: A review. Biotechnology Advances, 2016, 34(5): 1030–1045

[11] Melo P S, Maria S S, Vidal B C, Haun M, Durán N. Violacein cytotoxicity and induction of apoptosis in V79 cells. In Vitro Cellular & Developmental Biology, 2000, 36(8): 539–543

[12] Konzen M, De Marco D, Cordova C A S, Vieira T O, Antônio R V, Creczynski-Pasa T B. Antioxidant properties of violacein: Possible relation on its biological function. Bioorganic & Medicinal Chemistry, 2006, 14(24): 8307–8313

[13] Durán N, Antonio R V, Haun M, Pilli R A. Biosynthesis of a trypanocide by Chromobacterium violaceum. World Journal of Microbiology & Biotechnology, 1994, 10(6): 686–690

[14] Antonisamy P, Ignacimuthu S. Immunomodulatory, analgesic and antipyretic effects of violacein isolated from Chromobacterium violaceum. Phytomedicine, 2010, 17(3–4): 300–304

[15] Lee M E, Aswani A, Han A S, Tomlin C J, Dueber J E. Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay. Nucleic Acids Research, 2013, 41(22): 10668–10678

[16] Lin Q, Jia B, Mitchell L A, Luo J C, Yang K, Zeller K I, Zhang W Q, Xu Z W, Stracquadanio G, Bader J S, Boeke J D, Yuan Y J. 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

[17] Liu D, Liu H, Li B Z, Qi H, Jia B, Zhou X, Du H X, Zhang W, Yuan Y J. Multigene pathway engineering with regulatory linkers (M-PERL). ACS Synthetic Biology, 2016, 5(12): 1535–1545

[18] Knaggs A R. The biosynthesis of shikimate metabolites. Natural Product Reports, 2003, 20(1): 119–136

[19] Zalatan J G, Lee M, Almeida E R, Gilbert L A, Whitehead E H, La Russa M, Tsai J C, Weissman J S, Dueber J E, Qi L S, Lim W A. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell, 2015, 160(1–2): 339–350

[20] Jia B, Wu Y, Li B Z, Mitchell L A, Liu H, Pan S, Wang J, Zhang H R, Liu H M, Chen Z X, Precise control of SCRaMbLE in synthetic haploid and diploid yeast. Nature Communications, 2018, 9(1): 1933

[21] Querol A, Fernández-Espinar M T, Del Olmo M, Barrio E. Adaptive evolution of wine yeast. International Journal of Food Microbiology, 2003, 86(1–2): 3–10

[22] Gatti L, Hoe K L, Hayles J, Righetti S C, Carenini N B, Laura D, Kim D U, Park H O, Perego P. Ubiquitin-proteasome genes as targets for modulation of cisplatin sensitivity in fission yeast. BMC Genomics, 2011, 12(1): 44

[23] Dodgson S E, Santaguida S, Kim S, Sheltzer J, Amon A. The pleiotropic deubiquitinase UBP3 confers aneuploidy tolerance. Genes & Development, 2016, 30(20): 2259–2271

[24] Liu D, Li B Z, Liu H, Guo X J, Yuan Y J. Profiling influences of gene overexpression on heterologous resveratrol production in Saccharomyces cerevisiae. Frontiers of Chemical Science and Engineering, 2017, 11(1): 117–125

[25] Wang R Z, Gu X L, Yao M D, Pan C H, Liu H, Xiao W H, Wang Y, Yuan Y J. Engineering of β-carotene hydroxylase and ketolase for astaxanthin overproduction in Saccharomyces cerevisiae. Frontiers of Chemical Science and Engineering, 2017, 11(1): 89–99

[26] Yuan Y J, Wu J C, Wang X. Collaborations of China with the world in Synbio. Frontiers of Chemical Science and Engineering, 2017, 11(1): 1–2

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