成果及论文 - 代谢工程与合成生物学实验室

1. Qun Yue#, Jie Meng#, Yue Qiu, Miaomiao Yin, Liwen Zhang, Weiping Zhou, Zhiqiang An, Zihe Liu, Qipeng Yuan, Wentao Sun, Chun Li, István Molnár*, Yuquan Xu*, Shuobo Shi* (2023) A polycistronic system for multiplexed and precalibrated expression of multigene pathways in fungi. Nat Commun, 14: 4267.
2. Nailing Qi, Wentao Ding, Genlai Dong, Zhihui Wang, Shuobo Shi* (2023) De novo bio-production of odd-chain fatty acids in Saccharomyces cerevisiae through a synthetic pathway via 3-hydroxypropionic acid. Biotechnol. Bioeng. 120: 852-858. (TOP)
3. Shijie Xu, Weibo Qiao, Zuanwen Wang, Xiaoying Fu, Zihe Liu, Shuobo Shi* (2023). Exploiting a heterologous construction of the 3-hydroxypropionic acid carbon fixation pathway with mesaconate as an indicator in Saccharomyces cerevisiae. Bioresources and Bioprocessing. 10: 33
4. Jie Meng, Yue Qiu, Yueping Zhang, Huimin Zhao, Shuobo Shi* (2023) CMI: CRISPR/Cas9 based efficient multiplexed integration in Saccharomyces cerevisiae. ACS Synthetic Biology. 12: 1408 (cover paper) (TOP)
5. Juan Octavio Valle-Rodríguez, Verena Siewers, Jens Nielsen, Shuobo Shi* (2023). Directed evolution of a wax ester synthase for production of fatty acid ethyl esters in Saccharomyces cerevisiae. Applied Microbiology and Biotechnology, 2023, DOI : 10.1007/s00253-023-12466-8. (TOP)
6. Ning Qin, Lingyun Li, Zheng Wang, Shuobo Shi* (2023) Microbial production of odd-chain fatty acids. Biotechnol. Bioeng. https://doi.org/10.1002/bit.28308 (TOP)
7. Ning Qin, Lingyun Li, Xu Ji, Rui Pereira, Yu Chen, Shile Yin, Chaokun Li, Xiaozhen Wan, Danye Qiu, Junfeng Jiang, Hao Luo, Yueping Zhang, Genlai Dong, Yiming Zhang, Shuobo Shi, Henning J. Jessen, Jianye Xia, Yun Chen, Christer Larsson, Tianwei Tan, Zihe Liu, Jens Nielsen. (2023) Flux regulation through glycolysis and respiration is balanced by inositol pyrophosphates in yeast. Cell, https://doi.org/10.1016/j.cell.2023.01.014. (TOP)
8. Yi Yu, Shuobo Shi* (2023). Development and perspective of Rhodotorula toruloides as an efficient cell factory. Journal of Agricultural and Food Chemistry, 71: 1802–1819. (TOP)
9. Xiao Guo, Shuobo Shi* (2023). De novo genome sequencing and assembly of Rhodosporidium toruloides ∆dao1e strain. Microbiology Resource Announcements. https://doi.org/10.1128/mra.00600-22
10. Xiao Guo, Zhenzhen Bai, Yang Zhang, Shuobo Shi* (2023) Mining and Application of Constitutive Promoters from Rhodosporidium toruloides. AMB Express, 13: 17
11. 史硕博, 张翀, 成喜雨, 邢新会. (2023) 挑战造物主：合成生物学使能工具. 合成生物学, 4:1-4.
12. 王钻文，刘子鹤，史硕博* (2023). 新工科视域下生物工程专业教学与人才培养探索. 西南师范大学学报(自然科学版),. 48:111.
Zuanwen Wang, Zihe Liu, Shuobo Shi* (2023) Teaching Exploration and Talent Cultivation of Bioengineering Major from the Perspective of New Engineering Education. Journal of Southwest China Normal University, 48:111.
13. 史硕博，王禹博，乔玮博，吴龙昊，刘子鹤，谭天伟 (2023). 第三代生物炼制的挑战与机遇. 科学通报, https://doi.org/10.1360/TB-2022-1210.. (EI收录)
Shuobo Shi，Yubo Wang，Weibo Qiao，Longhao Wu，Zihe Liu，Tianwei Tan (2023) Challenges and opportunities in the third-generation biorefinery. Chinese Science Bulletin, Accepted.
14. 傅晓莹, 乔玮博, 史硕博* (2023). 微生物利用一碳底物生产单细胞蛋白. 食品科学, 44:1. (EI收录)
Xiaoying Fu, Weibo Qiao, Shuobo Shi* (2023) Adoption of the single carbon substrates to produce single-cell proteins from microbes. Food science. 44:1. (Indexed in EI)
15. 滕小龙, 史硕博* (2023). "CRISPR/Cas9系统在基因组编辑中的优化与发展." 合成生物学, 4: 67-85 (封面文章).
Xiaolong Teng, Shuobo Shi* (2023) Optimization and development of CRISPR/Cas9 systems for genome editing. Synthetic Biology Journal, 4: 67-85 (cover paper).
16. Faying Zhang, Xian Fan, Ke Xu, Shihui Wang, Shuobo Shi, Li Yi*, and Guimin Zhang* (2023) Development of a Bacterial FhuD-Lysozyme-SsrA Mediated Autolytic (FLSA) System for Effective Release of Intracellular Products. ACS Synthetic Biology, 12: 196 (TOP)
17. Weibo Qiao, Shijie Xu, Zihe Liu, Xiao.Fu, Huimin Zhao, Shuobo Shi* (2022). Challenges and opportunities in C1-based biomanufacturing. Bioresour. Technol. 364: 128095. (TOP)
18. Liyang Wang, Jinyu Fu, Guang Cai, Di Zhang, Shuobo Shi*, Yueping Zhang (2022) Rapid and Visual RPA-Cas12a Fluorescence Assay for Accurate Detection of Dermatophytes in Cats and Dogs. Biosensors 12(8), 636.
19. Weibo Qiao, Genlai Dong, Shijie Xu, Lingyun Li, Shuobo Shi* (2022) Engineering propionyl-CoA pools for de novo biosynthesis of odd-chain fatty acids in microbial cell factories. Critical Reviews in Biotechnology. doi: 10.1080/07388551.2022.2100736. (TOP)
20. Wentao Ding, Qiongyu Meng, Genlai Dong, NailingQi, Huimin Zhao*, Shuobo Shi* (2022) Metabolic engineering of threonine catabolism enables Saccharomyces cerevisiae to produce propionate under aerobic conditions. Biotechnology Journal, 17:2100579. (ESI Highly Cited Papers)
21. Xiyu Cheng, Ying Luo, Yifan Gao, Shen Li, Chunming Xu, Shangyuan Tang, Yongkun Yang, Zehua Zhang, He Jiang, Hanli Xu, Shuobo Shi*, Qiong Yan* (2022) Surfactant-assisted alkaline pretreatment and enzymatic hydrolysis of Miscanthus sinensis for enhancing sugar recovery with a reduced enzyme loading. Front. Bioeng. Biotechnol. 10:918126. doi: 10.3389/fbioe.2022.918126
22. Guang Cai, Zhenqun Lin, Shuobo Shi* (2022) Development and Expansion of the CRISPR/Cas9 Toolboxes for Powerful Genome Engineering in Yeast. Enzyme and Microbial Technology. 159, 110056
23. Shuobo Shi*, Jingyu Wang*, Hua Ling* (2022) Editorial: Synthetic biology for the sustainable production of biochemicals in engineered microbes. Front. Bioeng. Biotechnol. 10:984875. doi: 10.3389/fbioe.2022.984875
24. Yang Sun, Meilin Kong, Xiaowei Li, Qi Li, Qian Xue, Junyan Hou, Zefang Jia, Zhipeng Lei, Wei Xiao, Shuobo Shi*, Limin Cao* (2022) Metabolic and evolutionary engineering of diploid yeast for the production of first- and second- generation ethanol. Frontiers in Bioengineering and Biotechnology, 9: 835928.
25. Shuobo Shi, Zhihui Wang, Lirong Shen, Han Xiao (2022) Synthetic biology: pushing the new frontier of food production. Trends in Biotechnology. 40: 781. (TOP)
26. Yang Zhang, Xiao Guo, Huaiyi Yang, Shuobo Shi* (2022) The studies in constructing yeast cell factories for the production of fatty acid alkyl esters. Frontiers in Bioengineering and Biotechnology. 9:799032.
27. Shuobo Shi, Nailing Qi, Jens Nielsen (2022) Microbial production of chemicals driven by CRISPR-Cas systems. Current Opinion in Biotechnology, 73, 34-42. (TOP)
28. Yang Zhang, Jie Peng, Huimin Zhao, Shuobo Shi* (2021) Engineering Oleaginous Yeast Rhodotorula toruloides for Overproduction of Fatty Acid Ethyl Esters. Biotechnology for Biofuels, 14:115. (TOP)
29. Jinyu Fu, Yueping Zhang, Guang Cai, Geng Meng, Shuobo Shi* (2021) Rapid and sensitive RPA-Cas12a-fluorescence assay for point-of-care detection of African swine fever virus. PloS ONE, 16, e0254815.
30. Zhenquan Lin, Kang Xu, Guang Cai, Yangqingxue Liu, Yi Li, Zhihao Zhang, Jens Nielsen, Shuobo Shi*, Zihe Liu* (2021) Characterization of cross-species transcription and splicing from Penicillium to S. cerevisiae. J. Ind. Microbiol. Biotechnol., 48:kuab054.
31. Jinyu Fu, Junjie Li, Jing Chen, Yabei Li, Jiajia Liu, Xin Su, Shuobo Shi* (2021) Ultra-specific Nucleic Acid Testing by Target Activated Nucleases. Critical Reviews in Biotechnology, 42: 1061-1078 (TOP)
32. Guiping Gong, Yueping Zhang, Zibai Wang, Luo Liu, Shuobo Shi, Verena Siewers, Qipeng Yuan, Jens Nielsen, Xu Zhang, Zihe Liu (2021) GTR 2.0: gRNA-tRNA Array and Cas9-NG Based Genome Disruption and Single-Nucleotide Conversion in Saccharomyces cerevisiae. ACS Synthetic Biology. 10, 1328. (TOP)
33. Menglin Xiao, Niuniu Chen, Chengzhi He, Shuobo Shi, Qinfu Lu, and Shanshan Lv (2021) Generation of Yeast Protoplasts by Lytic Actions of Iron Oxide Magnetic Nanoparticles. Industrial & Engineering Chemistry Research. 60, 9012.
34. Zihe Liu, Hamideh Moradi, Shuobo Shi*, Farshad Darvishi (2021) Yeasts as microbial cell factories for sustainable production of biofuels. Renewable & Sustainable Energy Reviews. 143, 110907. (TOP)
35. Yiming Zhang, Shuobo Shi* (2021) Transcription factor-based biosensor for dynamic control in yeast for natural product synthesis. Frontiers in Bioengineering and Biotechnology. 9, 635265.
36. 史硕博, 赵颖, 杨田田, 赵梓含. (2021) 高校教师与研究生党支部共建体系的分析. 吉林省教育学院学报. 37:486
37. Yang Zhang, Wentao Ding, Zhihui Wang, Huimin Zhao*, Shuobo Shi* (2021) Development of host-orthogonal genetic systems for synthetic biology. Advanced Biology. 5, 2000252. (Back Cover)
38. Jie Meng, Yue Qiu, Shuobo Shi* (2020) CRISPR/Cas9 systems for the development of Saccharomyces cerevisiae cell factories. Frontiers in Bioengineering and Biotechnology, 8, 594347.
39. Wentao Ding, Yang Zhang, Shuobo Shi* (2020) Development and application of CRISPR/Cas in microbial biotechnology. Frontiers in Bioengineering and Biotechnology, 8:711.
40. 肖一凡, 彭杰, 张扬, 史硕博* (2020) 蜡酯合成酶的研究进展及其应用. 北京化工大学学报（自然科学版）. 47: 106
Yifan Xiao, Jie Peng, Yang Zhang, Shuobo Shi* (2020) Research progress and application of wax ester synthase. Journal of Beijing University of Chemical Technology (Natural Science), 47(6), 106
41. 史硕博, 孟琼宇, 乔玮博, 赵惠民 (2020) 塑造低碳经济的第三代固碳生物炼制. 合成生物学, 1:44-59.
Shuobo Shi, Qiongyu Meng, Weibo Qiao, Huimin Zhao (2020) Establishing Carbon Dioxide-based Third-generation Biorefinery for a Sustainable Low-carbon Economy. Synthetic Biology Journal, 1:44-59
42. Yueping Zhang#, Juan Wang#, Zibai Wang, Yiming Zhang, Shuobo Shi, Jens Nielsen, Zihe Liu* (2019) A gRNA-tRNA-array CRISPR/Cas9 (GTR-CRISPR) system for rapid and efficient mutiplexed genome editing in Saccharomyces cerevisiae. Nature Communications, 10:1053. (ESI Highly Cited Papers) (TOP)
43. Liang Xu, Cheng Tang, Xin Li, Xiaofan Li, Huiping Yang, Ruizhi Mao, Jiahui He, Wanqing Li, Jiyang Liu, Yalong Li, Shuobo Shi, Xuefeng Xiao*, Xianhua Wang* (2019) Ligand fishing with cellular membrane-coated cellulose filter paper: a new method for screening of potential active compounds from natural products. Anal Bioanal Chem, 411:1989.
44. Shuobo Shi, Ee Lui Ang, and Huimin Zhao (2018) In vivo Biosensors: Mechanisms, Development, and Applications. Journal of Industrial Microbiology & Biotechnology, 45:491.
45. Shuobo Shi, and Huimin Zhao (2017) Metabolic engineering of oleaginous yeasts for production of fuels and chemicals. Frontiers in Microbiology, 8:2185. (TOP)
46. Shuobo Shi, Youyun Liang, Ee Lui Ang, and Huimin Zhao* (2019) Delta integration CRISPR-Cas (Di-CRISPR) in Saccharomyces cerevisiae. Methods in Molecular Biology, 1927:73.
47. Shuobo Shi, Yook Wah Choi, Huimin Zhao, Tan Meng How, and Ee Lui Ang (2017) Discovery and engineering of a 1-butanol biosensor in Saccharomyces cerevisiae. Bioresource Technology, 245: 1343-1351. (TOP)
48. Shuobo Shi, Tong Si, Zihe Liu, Hongfang Zhang, Ee Lui Ang, and Huimin Zhao (2016) Metabolic engineering of a synergistic pathway for n-butanol production in Saccharomyces cerevisiae. Scientific Reports, 6:25675.
49. Shuobo Shi, Youyun Liang, Mingzi M Zhang, Ee Lui Ang, and Huimin Zhao (2016) A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae. Metabolic Engineering, 33:19-27. (ESI Highly Cited Papers) (TOP)
50. Shuobo Shi, Haichuan Ji, Verena Siewers, and Jens Nielsen (2016) Improved production of fatty acids by Saccharomyces cerevisiae through screening a cDNA library from the oleaginous yeast Yarrowia lipolytica. FEMS Yeast Research, 16(1): 108.
51. Bouke Wim de Jong, Shuobo Shi, Juan Octavio Valle-Rodríguez, Verena Siewers, and Jens Nielsen (2015) Metabolic pathway engineering for fatty acid ethyl ester production in Saccharomyces cerevisiae using stable chromosomal integration. Journal of Industrial Microbiology & Biotechnology, 42:477-86.
52. Shuobo Shi, Juan Octavio Valle-Rodríguez, Verena Siewers, and Jens Nielsen (2014) Engineering of chromosomal wax ester synthase integrated Saccharomyces cerevisiae mutants for improved biosynthesis of fatty acid ethyl esters. Biotechnology and Bioengineering, 111: 1740–1747. (TOP)
53. Shuobo Shi, Yun Chen, Verena Siewers, and Jens Nielsen (2014) Improving production of malonyl-CoA derived metabolites by abolishing Snf1-dependent regulation of Acc1. mBio, 5(3): e01130-14. (TOP)
54. Juan Octavio Valle-Rodríguez#, Shuobo Shi#, Verena Siewers, and Jens Nielsen (2014) Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid ethyl esters, and advanced biofuel, by eliminating non-essential fatty acid utilization pathways. Applied Energy, 115: 226-232. (#contributed equally) (ESI Highly Cited Papers) (TOP)
55. Bouke Wim de Jong, Shuobo Shi, Verena Siewers, and Jens Nielsen (2014) Improved production of fatty acid ethyl esters in Saccharomyces cerevisiae through up-regulation of the ethanol degradation pathway and expression of the heterologous phosphoketolase pathway. Microbial Cell Factories, 13: 39.
56. Shuobo Shi, Tao Chen, and Xueming Zhao (2013) Comparative transcriptome analysis for metabolic engineering. Methods in Molecular Biology, 985: 447-458.
57. Shuobo Shi, Juan Octavio Valle-Rodríguez, Sakda Khoomrung, Verena Siewers, and Jens Nielsen (2012) Functional expression and characterization of five wax ester synthases in Saccharomyces cerevisiae and their utility for biodiesel production. Biotechnology for Biofuels 5: 7. (TOP)
58. Shuobo Shi, Juan Octavio Valle-Rodríguez, Verena Siewers, and Jens Nielsen (2011) Prospects for microbial biodiesel production. Biotechnology Journal, 6: 277-285.
59. Shuobo Shi, Tao Chen, and Xueming Zhao (2010) Transcriptome platforms and applications to metabolic engineering. Chinese Journal of Biotechnology 26: 1187-1198.
60. Shuobo Shi, Tao Chen, Zhigang Zhang, Xun Chen, and Xueming Zhao (2009) Transcriptome analysis guided metabolic engineering of Bacillus subtilis for riboflavin production. Metabolic Engineering, 11: 243-252. (TOP)
61. Shuobo Shi, Zhuo Shen, Xun Chen, Tao Chen, and Xueming Zhao (2009) Increased production of riboflavin by metabolic engineering of the purine pathway in Bacillus subtilis. Biochemical Engineering Journal, 46: 28-33.
62. Shuobo Shi, Tao Chen, Xun Chen, Qiuli Wu, Yu Gan, and Xueming Zhao (2008) Abolishing the imbalance supply of precursors in Bacillus subtilis RH44 to increase riboflavin production. Journal of Biotechnology, 136S:S36.
63. Shuobo Shi, Tao Chen, Xun Chen, Qiuli Wu, Yu Gan, and Xueming Zhao (2008) Enhancing riboflavin production by genetic modification of purine pathway in Bacillus subtilis. Journal of Biotechnology, 136S:S35.
64. Yingbo Zhu, Xun Chen, Tao Chen, Shuobo Shi, and Xueming Zhao (2006) Over-expression of glucose dehydrogenase improves cell growth and riboflavin production in Bacillus subtilis. Biotechnology Letters, 28:1667-1672.
65. Shuobo Shi, Hongfang Zhang, Ee Lui Ang, Huimin Zhao (2016) High throughput screening or selection methods for evolutionary enzyme engineering. In: Understanding enzymes: Function, Design, Engineering and Analysis. A. Svendsen (Ed.), PanStandford Publishing.
66. Shuobo Shi (2008) Bioprocess considerations in using animal cell cultures. In: Bioprocess Engineering: Basic Concepts. Tao Chen, et al. (Ed), Chemical Engineering Press, Beijing, China.