Genome shuffling for phenotypic improvement of industrial strains through recursive protoplast fusion technology

References

• Biot-Pelletier, D., and V. J. J. Martin. 2014. Evolutionary engineering by genome shuffling. Applied Microbiology and Biotechnology 98 (9):3877–87. doi: 10.1007/s00253-014-5616-8.
   PubMed Web of Science ®Google Scholar
• Bode, H. B., and R. Müller. 2006. Analysis of myxobacterial secondary metabolism goes molecular. Journal of Industrial Microbiology & Biotechnology 33 (7):577–88. doi: 10.1007/s10295-006-0082-7.
   PubMed Web of Science ®Google Scholar
• Cao, X., L. Hou, M. Lu, C. Wang, and B. Zeng. 2010. Genome shuffling of Zygosaccharomyces rouxii to accelerate and enhance the flavour formation of soy sauce. Journal of the Science of Food and Agriculture 90 (2):281–5. doi: 10.1002/jsfa.3810.
   PubMed Web of Science ®Google Scholar
• Cao, X., Q. Song, C. Wang, and L. Hou. 2012. Genome shuffling of Hansenula anomala to improve flavour formation of soy sauce. World Journal of Microbiology & Biotechnology 28 (5):1857–62. doi: 10.1007/s11274-010-0477-5.
   PubMed Web of Science ®Google Scholar
• Chen, T., J. Wang, S. Zhou, X. Chen, R. Ban, and X. Zhao. 2004. Trait improvement of riboflavin-producing Bacillus subtilis by genome shuffling and metabolic flux analysis. Journal of Chemical Industry and Engineering 55:1842–8.
   Google Scholar
• Cheng, Y., X. Song, Y. Qin, and Y. Qu. 2009. Genome shuffling improves production of cellulase by Penicillium decumbens JU-A10. Journal of Applied Microbiology 107 (6):1837–46. doi: 10.1111/j.1365-2672.2009.04362.x.
   PubMed Web of Science ®Google Scholar
• Dai, M. H., and S. D. Copley. 2004. Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723. Applied and Environmental Microbiology 70 (4):2391–7. doi: 10.1128/AEM.70.4.2391-2397.2004.
   PubMed Web of Science ®Google Scholar
• del Cardayré, S. B. 2005. Developments in strain improvement technology: Evolutionary engineering of industrial microorganisms through gene, pathway, and genome shuffling. In Natural Products - Drug Discovery and Therapeutic Medicine, eds. L. Zhang, and A. L. Demain, 107–25. New York: Humana Press Inc.
   Google Scholar
• Demeke, M. M., H. Dietz, Y. Li, M. R. Foulquié-Moreno, S. Mutturi, S. Deprez, T. Den Abt, B. M. Bonini, G. Liden, F. Dumortier, et al. 2013. Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering. Biotechnology for Biofuels 6 (1):1–24. doi: 10.1186/1754-6834-6-89.
   PubMedGoogle Scholar
• El-Bondkly, A. M. A. 2012. Molecular identification using its sequences and genome shuffling to improve 2-deoxyglucose tolerance and xylanase activity of marine-derived fungus, Aspergillus sp. NRCF5. Applied Biochemistry and Biotechnology 167 (8):2160–73. doi: 10.1007/s12010-012-9763-z.
   PubMed Web of Science ®Google Scholar
• Gong, G-l, X. Sun, X-l Liu, W. Hu, W-R Cao, H. Liu, W-F Liu, and Y-Z Li. 2007. Mutation and a high-throughput screening method for improving the production of Epothilones of Sorangium. Journal of Industrial Microbiology & Biotechnology 34 (9):615–23. doi: 10.1007/s10295-007-0236-2.
   PubMed Web of Science ®Google Scholar
• Gong, J., H. Zheng, Z. Wu, T. Chen, and X. Zhao. 2009. Genome shuffling: Progress and applications for phenotype improvement. Biotechnology Advances 27 (6):996–1005. doi: 10.1016/j.biotechadv.2009.05.016.
   PubMed Web of Science ®Google Scholar
• Gong, J., X. Zhao, Q. Xing, F. Li, H. Li, Y. Li, L. Chai, Q. Wang, and A. Zheltikov. 2008. Femtosecond laser-induced cell fusion. Applied Physics Letters 92 (9):093901–4. doi: 10.1063/1.2890070.
   Web of Science ®Google Scholar
• Graves, T., N. V. Narendranath, K. Dawson, and R. Power. 2007. Interaction effects of lactic acid and acetic acid at different temperatures on ethanol production by Saccharomyces cerevisiae in corn mash. Applied Microbiology and Biotechnology 73 (5):1190–6. doi: 10.1007/s00253-006-0573-5.
   PubMed Web of Science ®Google Scholar
• Guan, N., L. Liu, X. Zhuge, Q. Xu, J. Li, G. Du, and J. Chen. 2012. Genome shuffling improves acid tolerance of Propionibacterium acidipropionici and propionic acid production. Advances in Chemistry Research 15:143–52.
   Google Scholar
• Hida, H., T. Yamada, and Y. Yamada. 2005. Production of hydroxycitric acid by microorganisms. Bioscience, Biotechnology and Biochemistry 69 (8):1555–61. doi: 10.1271/bbb.69.1555.
   PubMed Web of Science ®Google Scholar
• Hida, H., T. Yamada, and Y. Yamada. 2006. Absolute configuration of hydroxycitric acid produced by microorganisms. Bioscience, Biotechnology and Biochemistry 70 (8):1972–4. doi: 10.1271/bbb.50701.
   PubMed Web of Science ®Google Scholar
• Hida, H., T. Yamada, and Y. Yamada. 2007. Genome shuffling of Streptomyces sp. U121 for improved production of hydroxycitric acid. Applied Microbiology and Biotechnology 73 (6):1387–93. doi: 10.1007/s00253-006-0613-1.
   PubMed Web of Science ®Google Scholar
• Hou, L. 2010. Improved production of ethanol by novel genome shuffling in Saccharomyces cerevisiae. Applied Biochemistry and Biotechnology 160 (4):1084–93. doi: 10.1007/s12010-009-8552-9.
   PubMed Web of Science ®Google Scholar
• Jin, Z. H., B. Xu, S. Z. Lin, Q. C. Jin, and P. L. Cen. 2009. Enhanced production of spinosad in Saccharopolyspora spinosa by genome shuffling. Applied Biochemistry and Biotechnology 159 (3):655–63. doi: 10.1007/s12010-008-8500-0.
   PubMed Web of Science ®Google Scholar
• Jingping, G., S. Hongbing, S. Gang, L. Hongzhi, and P. Wenxiang. 2012. A genome shuffling-generated Saccharomyces cerevisiae isolate that ferments xylose and glucose to produce high levels of ethanol. Journal of Industrial Microbiology & Biotechnology 39 (5):777–87. doi: 10.1007/s10295-011-1076-7.
   PubMed Web of Science ®Google Scholar
• John, R. P., D. Gangadharan, and K. Madhavan Nampoothiri. 2008. Genome shuffling of Lactobacillus delbrueckii mutant and Bacillus amyloliquefaciens through protoplasmic fusion for l-lactic acid production from starchy wastes. Bioresource Technology 99 (17):8008–15. doi: 10.1016/j.biortech.2008.03.058.
   PubMed Web of Science ®Google Scholar
• John, R. P., G. S. Anisha, A. Pandey, and K. Madhavan. 2010. Genome shuffling: A new trend in improved bacterial production of lactic acid. Industrial Biotechnology 6 (3):164–70. doi: 10.1089/ind.2010.6.164.
   Google Scholar
• Kawahata, M., T. Fujii, and H. Iefuji. 2007. Intraspecies diversity of the industrial yeast strains Saccharomyces cerevisiae and Saccharomyces pastorianus based on analysis of the sequences of the internal transcribed spacer (ITS) regions and the D1/D2 region of 26S rDNA. Bioscience, Biotechnology and Biochemistry 71 (7):1616–20. doi: 10.1271/bbb.60673.
   PubMed Web of Science ®Google Scholar
• Kumar, M., M. P. Singh, and D. K. Tuli. 2012. Genome shuffling of Pseudomonas sp. Ioca11 for improving degradation of polycyclic aromatic hydrocarbons. Advances in Microbiology 2 (1):26–30. doi: 10.4236/aim.2012.21004.
   Google Scholar
• Leja, K., K. Myszka, and K. Czaczyk. 2011. Genome shuffling: A method to improve biotechnological processes. Biotechnologia 92 (4):345–51. doi: 10.5114/bta.2011.46551.
   Google Scholar
• Li, H., F. Xue, W. Wang, and B. Chen. 2015. Genome shuffling of Lactobacillus brevis for enhanced production of thymidine phosphorylase. Biotechnology and Bioprocess Engineering 20 (2):333–40. doi: 10.1007/s12257-014-0617-0.
   Web of Science ®Google Scholar
• Li, S., F. Li, X. S. Chen, L. Wang, J. Xu, L. Tang, and Z. G. Mao. 2012. Genome shuffling enhanced ε-poly-l-lysine production by improving glucose tolerance of Streptomyces graminearus. Applied Biochemistry and Biotechnology 166 (2):414–23. doi: 10.1007/s12010-011-9437-2.
   PubMed Web of Science ®Google Scholar
• Liang, H., and Y. Guo. 2006. Whole genome shuffling to enhance activity of fibrinolytic enzyme-producing strains. China Biotechnology 27:39–43.
   Google Scholar
• Lin, J., B. H. Shi, Q. Q. Shi, Y. X. He, and M. Z. Wang. 2007. Rapid improvement of lipase production in Penicillium expansum by genome shuffling. Chinese Journal of Biotechnology 23 (4):672–6. doi: 10.1016/s1872-2075(07)60044-2.
   Google Scholar
• Luo, J. M., J. S. Li, D. Liu, F. Liu, Y. T. Wang, X. R. Song, and M. Wang. 2012. Genome shuffling of Streptomyces gilvosporeus for improving natamycin production. Journal of Agricultural and Food Chemistry 60 (23):6026–36. doi: 10.1021/jf300663w.
   PubMed Web of Science ®Google Scholar
• Lv, X. A., Y. Y. Jin, Y. D. Li, H. Zhang, and X. L. Liang. 2013. Genome shuffling of Streptomyces viridochromogenes for improved production of avilamycin. Applied Microbiology and Biotechnology 97 (2):641–8. doi: 10.1007/s00253-012-4322-7.
   PubMed Web of Science ®Google Scholar
• Mao, F. L., Q. R. Xing, K. Wang, L. Y. Lang, Z. Wang, L. Chai, and Q. Y. Wang. 2005. Optical trapping of red blood cells and two-photon excitation-based photodynamic study using a femtosecond laser. Optics Communications 256 (4–6):358–63. doi: 10.1016/j.optcom.2005.06.076.
   Web of Science ®Google Scholar
• Máté de Gérando, H., F. Fayolle-Guichard, L. Rudant, S. K. Millah, F. Monot, N. Lopes Ferreira, and A. M. López-Contreras. 2016. Improving isopropanol tolerance and production of Clostridium beijerinckii DSM 6423 by random mutagenesis and genome shuffling. Applied Microbiology and Biotechnology 100 (12):5427–36. doi: 10.1007/s00253-016-7302-5.
   PubMed Web of Science ®Google Scholar
• Otte, B., E. Grunwaldt, O. Mahmoud, and S. Jennewein. 2009. Genome shuffling in Clostridium diolis DSM 15410 for improved 1,3-propanediol production. Applied and Environmental Microbiology 75 (24):7610–6. doi: 10.1128/AEM.01774-09.
   PubMed Web of Science ®Google Scholar
• Patnaik, R., S. Louie, V. Gavrilovic, K. Perry, W. P. C. Stemmer, C. M. Ryan, and S. Del Cardayré. 2002. Genome shuffling of Lactobacillus for improved acid tolerance. Nature Biotechnology 20 (7):707–12. doi: 10.1038/nbt0702-707.
   PubMed Web of Science ®Google Scholar
• Petri, R., and C. Schmidt-Dannert. 2004. Dealing with complexity: Evolutionary engineering and genome shuffling. Current Opinion in Biotechnology 15 (4):298–304. doi: 10.1016/j.copbio.2004.05.005.
   PubMed Web of Science ®Google Scholar
• Pinel, D., F. D’Aoust, S. B. del Cardayre, P. K. Bajwa, H. Lee, and V. J. J. Martin. 2011. Saccharomyces cerevisiae genome shuffling through recursive population mating leads to improved tolerance to spent sulfite liquor. Applied and Environmental Microbiology 77 (14):4736–43. doi: 10.1128/AEM.02769-10.
   PubMed Web of Science ®Google Scholar
• Rassoulzadegan, M., B. Binetruy, and F. Cuzin. 1982. High frequency of gene transfer after fusion between bacteria and eukaryotic cells. Nature 295 (5846):257–9. doi: 10.1038/295257a0.
   PubMed Web of Science ®Google Scholar
• Shi, D. J., C. L. Wang, and K. M. Wang. 2009. Genome shuffling to improve thermotolerance, ethanol tolerance and ethanol productivity of Saccharomyces cerevisiae. Journal of Industrial Microbiology & Biotechnology 36 (1):139–47. doi: 10.1007/s10295-008-0481-z.
   PubMed Web of Science ®Google Scholar
• Shi, J., M. Zhang, L. Zhang, P. Wang, L. Jiang, and H. Deng. 2014. Xylose-fermenting Pichia stipitis by genome shuffling for improved ethanol production. Microbial Biotechnology 7 (2):90–9. doi: 10.1111/1751-7915.12092.
   PubMed Web of Science ®Google Scholar
• Shih, I. L., M. H. Shen, and Y. T. Van. 2006. Microbial synthesis of poly(epsilon-lysine) and its various applications. Bioresource Technology 97 (9):1148–59. doi: 10.1016/j.biortech.2004.08.012.
   PubMed Web of Science ®Google Scholar
• Skelley, A. M., O. Kirak, H. Suh, R. Jaenisch, and J. Voldman. 2009. Microfluidic control of cell pairing and fusion. Nature Methods 6 (2):147–52. doi: 10.1038/nmeth.1290.
   PubMed Web of Science ®Google Scholar
• Steensels, J., T. Snoek, E. Meersman, M. P. Nicolino, K. Voordeckers, and K. J. Verstrepen. 2014. Improving industrial yeast strains: Exploiting natural and artificial diversity. FEMS Microbiology Reviews 38 (5):947–95. doi: 10.1111/1574-6976.12073.
   PubMed Web of Science ®Google Scholar
• Sun, J., H. Li, Y. Ni, X. Zhang, J. Shi, and Z. Xu. 2017. Genome shuffling of Colletotrichum lini for improving 3β,7α,15α-trihydroxy-5-androsten-17-one production from dehydroepiandrosterone. Journal of Industrial Microbiology & Biotechnology 44 (6):937–47. doi: 10.1007/s10295-017-1918-z.
   PubMed Web of Science ®Google Scholar
• Tong, Q. Q., Y. H. Zhou, X. S. Chen, J. Y. Wu, P. Wei, L. X. Yuan, and J. M. Yao. 2018. Genome shuffling and ribosome engineering of Streptomyces virginiae for improved virginiamycin production. Bioprocess and Biosystems Engineering 41 (5):729–38. doi: 10.1007/s00449-018-1906-3.
   PubMed Web of Science ®Google Scholar
• Verma, V., G. N. Qazi, and R. Parshad. 1992. Intergeneric protoplast fusion between Gluconobacter oxydans and Corynebacterium species. Journal of Biotechnology 26 (2–3):327–30. doi: 10.1016/0168-1656(92)90016-3.
   PubMed Web of Science ®Google Scholar
• Wang, C., G. Wu, Y. Li, Y. Huang, F. Zhang, and X. Liang. 2013. Genome shuffling of Penicillium citrinum for enhanced production of nuclease P1. Applied Biochemistry and Biotechnology 170 (6):1533–45. doi: 10.1007/s12010-013-0297-9.
   PubMed Web of Science ®Google Scholar
• Wang, Y., Y. Li, X. Pei, L. Yu, and Y. Feng. 2007. Genome-shuffling improved acid tolerance and l-lactic acid volumetric productivity in Lactobacillus rhamnosus. Journal of Biotechnology 129 (3):510–5. doi: 10.1016/j.jbiotec.2007.01.011.
   PubMed Web of Science ®Google Scholar
• Wei, P., Z. Li, P. He, Y. Lin, and N. Jiang. 2008. Genome shuffling in the ethanologenic yeast Candida krusei to improve acetic acid tolerance. Biotechnology and Applied Biochemistry 49 (Pt 2):113–20. doi: 10.1042/BA20070072.
   PubMedGoogle Scholar
• Xu, B., Z. Jin, H. Wang, Q. Jin, X. Jin, and P. Cen. 2008. Evolution of Streptomyces pristinaespiralis for resistance and production of pristinamycin by genome shuffling. Applied Microbiology and Biotechnology 80 (2):261–7. doi: 10.1007/s00253-008-1540-0.
   PubMed Web of Science ®Google Scholar
• Xu, F., H. Jin, H. Li, L. Tao, J. Wang, J. Lv, and S. Chen. 2012. Genome shuffling of Trichoderma viride for enhanced cellulase production. Annals of Microbiology 62 (2):509–15. doi: 10.1007/s13213-011-0284-8.
   Web of Science ®Google Scholar
• Yu, G., Y. Hu, M. Hui, L. Chen, L. Wang, N. Liu, Y. Yin, and J. Zhao. 2014. Genome shuffling of Streptomyces roseosporus for improving daptomycin production. Applied Biochemistry and Biotechnology 172 (5):2661–9. doi: 10.1007/s12010-013-0687-z.
   PubMed Web of Science ®Google Scholar
• Yu, L., X. Pei, T. Lei, Y. Wang, and Y. Feng. 2008. Genome shuffling enhanced l-lactic acid production by improving glucose tolerance of Lactobacillus rhamnosus. Journal of Biotechnology 134 (1–2):154–9. doi: 10.1016/j.jbiotec.2008.01.008.
   PubMed Web of Science ®Google Scholar
• Zhang, G., Y. Lin, X. Qi, L. Wang, P. He, Q. Wang, and Y. Ma. 2015. Genome shuffling of the nonconventional yeast Pichia anomala for improved sugar alcohol production. Microbial Cell Factories 14 (1):1–10. doi: 10.1186/s12934-015-0303-8.
   PubMedGoogle Scholar
• Zhang, J., X. Wang, J. Diao, H. He, Y. Zhang, and W. Xiang. 2013. Streptomycin resistance-aided genome shuffling to improve doramectin productivity of Streptomyces avermitilis NEAU1069. Journal of Industrial Microbiology & Biotechnology 40 (8):877–89. doi: 10.1007/s10295-013-1280-8.
   PubMed Web of Science ®Google Scholar
• Zhang, Y., J. Z. Liu, J. S. Huang, and Z. W. Mao. 2010. Genome shuffling of Propionibacterium shermanii for improving vitamin B12 production and comparative proteome analysis. Journal of Biotechnology 148 (2-3):139–43. doi: 10.1016/j.jbiotec.2010.05.008.
   PubMed Web of Science ®Google Scholar
• Zhang, Y., K. Perry, V. A. Vinci, K. Powell, W. P. C. Stemmer, and S. B. Del Cardayré. 2002. Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 415 (6872):644–6. doi: 10.1038/415644a.
   PubMed Web of Science ®Google Scholar
• Zhao, K., W. X. Ping, L. N. Zhang, J. Liu, Y. Lin, T. Jin, and D. P. Zhou. 2008. Screening and breeding of high taxol producing fungi by genome shuffling. Science in China, Series C: Life Sciences 51 (3):222–31. doi: 10.1007/s11427-008-0037-5.
   PubMedGoogle Scholar
• Zheng, H., J. Gong, T. Chen, X. Chen, and X. Zhao. 2010. Strain improvement of Sporolactobacillus inulinus ATCC 15538 for acid tolerance and production of D-lactic acid by genome shuffling. Applied Microbiology and Biotechnology 85 (5):1541–9. doi: 10.1007/s00253-009-2243-x.
   PubMed Web of Science ®Google Scholar
• Zheng, P., K. Zhang, Q. Yan, Y. Xu, and Z. Sun. 2013. Enhanced succinic acid production by Actinobacillus succinogenes after genome shuffling. Journal of Industrial Microbiology & Biotechnology 40 (8):831–40. doi: 10.1007/s10295-013-1283-5.
   PubMed Web of Science ®Google Scholar
• Zheng, P., Liu, M. Liu, X.E., Du, Q.Y., Ni, Y. & Sun, Z.H.. 2012. Genome shuffling improves thermotolerance and glutamic acid production of Corynebacteria glutamicum. World Journal of Microbiology & Biotechnology 28 (3):1035–43. doi: 10.1007/s11274-011-0902-4.
   PubMed Web of Science ®Google Scholar
• Zhu, Z., X. Wu, B. Lv, G. Wu, J. Wang, W. Jiang, P. Li, J. He, J. Chen, M. Chen, et al. 2016. A new approach for breeding low-temperature resistant Volvariella volvacea strains: Genome shuffling in edible fungi Ziping. Biotechnology and Applied Biochemistry 63 (5):605–15. doi: 10.1002/bab.1420.
   PubMed Web of Science ®Google Scholar
• Zirkle, R., J. M. Ligon, and I. Molnár. 2004. Heterologous production of the antifugal polyketide antibiotic soraphen A of Sorangium cellulosum So ce26 in Streptomyces lividans. Microbiology 150 (8):2761–74. doi: 10.1099/mic.0.27138-0.
   PubMedGoogle Scholar