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.

Key words： synthetic biology; genome rearrangement; prodeoxyviolacein; SCRaMbLE; Saccharomyces cerevisiae

Acknowledgements

We thank the National Program on Key Basic Research Project of China (2014CB745100) and the National Natural Science Foundation of China (21750001 and 21621004) for funding.

Electronic Supplementary Material

Supplementary material is available in the online version of this article at https://doi.org/10.1007/s11705–018-1739-2 and is accessible for authorized users.

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