科学研究

（1）全细胞催化剂开发1-科学基础

红色红球菌超高有机溶剂耐受性和独特的外源酶尿素诱导高表达机制，被认为是最具发展潜力的工业生物技术平台菌株之一，可广泛应用于生物催化合成领域。课题组克服了红球菌基因组GC碱基含量过高(68.6-72.7％)、基因重组操作难度大、遗传工具匮乏等困难，成功建立了红色红球菌Crispr/Cas9基因组编辑方法和梯级强度启动子库，解析了其分子伴侣网络及高耐受性机制，发现了其菌落两型性机理，实现了质粒载体尿素诱导高表达及稳定遗传，为红球菌全细胞生物催化剂用于高效催化合成酰胺、羧酸和手性医药中间体奠定了基础。

 

（2）全细胞催化剂开发2-酶分子改造耦合及产业化应用

重组红球菌全细胞催化剂已经成功用于生物法高产丙烯酰胺。通过耦合盐桥和二硫桥改造的腈水合酶，TH系列高产丙烯酰胺重组红球菌具有高耐受性、低/无副产物、低电导率等优异性能，已在企业成功应用，合计增加总利润近5亿元，为国家上交税收约3.5亿元，创汇约1.5亿美元，且显著节能减排，经济和社会效益显著。目前，正在致力于开发红球菌全细胞生物催化剂作为平台细胞，广泛用于高效催化合成各种酰胺、羧酸和手性医药中间体。


 

（3）高效细胞工厂创制

枯草芽孢杆菌和谷氨酸棒杆菌具有良好的生物安全性和突出的目标产物高效合成能力。实验室致力于重组枯草芽孢杆菌和重组谷氨酸棒杆菌高效细胞工厂的创制及代谢工程调控，并实现了脂肽（表面活性素）、透明质酸、软骨素等生物大分子的高效合成。



 
 
 

（4）纳米生物技术

M13噬菌体是是丝状噬菌体家族中的一员，由于其天然的纳米级尺寸和特殊的吸附性质，已成为当今研究热点之一。课题组研究总结了噬菌体对金属离子的吸附规律，制备了多种以M13噬菌体为模板的单金属纳米颗粒和铁-镍、铁-铜双金属纳米颗粒。并设计构建了Fe-Ni@M13微电解体系，建立了M13噬菌体介导的酶固定化新方法。

Fe-Ni@M13 微电解体系

基于M13噬菌体的新型固定化酶方法开发

近10年发表的论文
 

1. Liang, Y.; Jiao, S.; Wang, M.; Yu, H.; Shen, Z., A CRISPR/Cas9-based genome editing system for Rhodococcus ruber TH. Metabolic Engineering 2019. DOI: 10.1016/j.ymben.2019.10.003.
2. Cheng, F. Y.; Yu, H. M.; Stephanopoulos, G., Engineering Corynebacterium glutamicum for high-titer biosynthesis of hyaluronic acid. Metabolic Engineering 2019, 55, 276-289.
3. Wang, M.; Qi, W.; Xu, H.; Yu, H.; Zhang, S.; Shen, Z., Affinity-binding immobilization of D-amino acid oxidase on mesoporous silica by a silica-specific peptide. Journal of industrial microbiology & biotechnology 2019.
4. Tang, L.; Yang, J.; Chen, J.; Zhang, J.; Yu, H.; Shen, Z., Design of salt-bridge cyclization peptide tags for stability and activity enhancement of enzymes. Process Biochemistry 2019, 81, 39-47.
5. Cheng, F.; Luozhong, S.; Yu, H.; Guo, Z., Biosynthesis of Chondroitin in Engineered Corynebacterium glutamicum. Journal of Microbiology and Biotechnology 2019, 29, (3), 392-400.
6. Wang, M.; Yu, H.; Shen, Z., Antisense RNA-Based Strategy for Enhancing Surfactin Production in Bacillus subtilis TS1726 via Overexpression of the Unconventional Biotin Carboxylase II To Enhance ACCase Activity. Acs Synthetic Biology 2019, 8, (2), 251-256.
7. Liang, Y.; Jiao, S.; Wang, M.; Yu, H.; Shen, Z., Overexpression of epoxide hydrolase in Rhodococcus ruber with high robustness for the synthesis of chiral epichlorohydrin. Process Biochemistry 2019, 79, 49-56.
8. Guo, M.; Yang, L.; Li, J.; Jiao, S.; Wang, Y.; Luo, G.; Yu, H., Effects of interface adsorption of Rhodococcus ruber TH3 cells on the biocatalytic hydration of acrylonitrile to acrylamide. Bioprocess and Biosystems Engineering 2018, 41, (7), 931-938.
9. Wang, M.; Chen, J.; Yu, H.; Shen, Z., Improving stress tolerance and cell integrity of Rhodococcus ruber by overexpressing small-shock-protein Hsp16 of Rhodococcus. Journal of Industrial Microbiology & Biotechnology 2018, 45, (10), 929-938.
10. Chen, Y.; Jiao, S.; Wang, M.; Chen, J.; Yu, H., A novel molecular chaperone GroEL2 from Rhodococcus ruber and its fusion chimera with nitrile hydratase for co-enhanced activity and stability. Chemical Engineering Science 2018, 192, 235-243.
11. Jiao, S.; Yu, H.; Shen, Z., Core element characterization of Rhodococcus promoters and development of a promoter-RBS mini-pool with different activity levels for efficient gene expression. New Biotechnology 2018, 44, 41-49.
12. Wang, Q.; Yu, H.; Wang, M.; Yang, H.; Shen, Z., Enhanced biosynthesis and characterization of surfactin isoforms with engineered Bacillus subtilis through promoter replacement and Vitreoscilla hemoglobin co-expression. Process Biochemistry 2018, 70, 36-44.
13. Cheng, F.; Luozhong, S.; Guo, Z.; Yu, H.; Stephanopoulos, G. J. B. J., Enhanced biosynthesis of hyaluronic acid using engineered Corynebacterium glutamicum via metabolic pathway regulation. 2017, 12, (10), 1700268.
14. Yang, J.; Cheng, F.; Yu, H.; Wang, J.; Guo, Z.; Stephanopoulos, G., Key Role of the Carboxyl Terminus of Hyaluronan Synthase in Processive Synthesis and Size Control of Hyaluronic Acid Polymers. Biomacromolecules 2017, 18, (4), 1064-1073.
15. Jiao, S.; Chen, J.; Yu, H.; Shen, Z., Tuning and elucidation of the colony dimorphism in Rhodococcus ruber associated with cell flocculation in large scale fermentation. Applied Microbiology and Biotechnology 2017, 101, (16), 6321-6332.
16. Zhang, S.; Yu, H.; Yang, J.; Shen, Z., Design of the nanoarray pattern Fe-Nibi-metal nanoparticles@M13 virus for the enhanced reduction of p-chloronitrobenzene through the micro-electrolysis effect. Environmental Science-Nano 2017, 4, (4), 876-885.
17. Li, J.; Guo, M.; Jiao, S.; Wang, Y.; Luo, G.; Yu, H., A kinetic study of the biological catalytic hydration of acrylonitrile to acrylamide. Chemical Engineering Journal 2017, 317, 699-706.
18. Jiao, S.; Li, X.; Yu, H.; Yang, H.; Li, X.; Shen, Z., In situ enhancement of surfactin biosynthesis in Bacillus subtilis using novel artificial inducible promoters. Biotechnology and Bioengineering 2017, 114, (4), 832-842.
19. Luo, H.; Zhu, L.; Chang, Y.; Liu, X.; Liu, Z.; Sun, H.; Li, X.; Yu, H.; Shen, Z., Microenvironmental pH changes in immobilized cephalosporin C acylase during a proton-producing reaction and regulation by a two-stage catalytic process. Bioresource Technology 2017, 223, 157-165.
20. Sun, J.; Yu, H.; Chen, J.; Luo, H.; Shen, Z., Ammonium acrylate biomanufacturing by an engineered Rhodococcus ruber with nitrilase overexpression and double-knockout of nitrile hydratase and amidase. Journal of Industrial Microbiology & Biotechnology 2016, 43, (12), 1631-1639.
21. Li, J.; Chen, Y.; Guo, M.; Wang, Y.; Xu, J.; Luo, G.; Yu, H., Using microchannels to visually investigate the formation and dissolution of acrylonitrile droplets in a bio-hydration system. Chemical Engineering Science 2016, 152, 239-247.
22. Wei, Y.; Luo, H.; Chang, Y.; Yu, H.; Shen, Z., Reversible immobilization of cephalosporin C acylase on epoxy supports coated with polyethyleneimine. Biocatalysis and Biotransformation 2015, 33, (5-6), 250-259.
23. Cheng, F.; Gong, Q.; Yu, H.; Stephanopoulos, G., High-titer biosynthesis of hyaluronic acid by recombinant Corynebacterium glutamicum. Biotechnology Journal 2016, 11, (4), 574-584.
24. Tian, Y.; Chen, J.; Yu, H.; Shen, Z. J. J. M. B., Overproduction of the Escherichia coli chaperones GroEL-GroES in Rhodococcus ruber improves the activity and stability of cell catalysts harboring a nitrile hydratase. 2015, 26, (2), 337.
25. Zhang, S.; Nakano, K.; Zhang, S.-l.; Yu, H.-m., Synthesis of dispersive iron or iron-silver nanoparticles on engineered capsid pVIII of M13 virus with electronegative terminal peptides. Journal of Nanoparticle Research 2015, 17, (10).
26. Luo, H.; Ma, J.; Chang, Y.; Yu, H.; Shen, Z., Directed Evolution and Mutant Characterization of Nitrilase from Rhodococcus rhodochrous tg1-A6. Applied Biochemistry and Biotechnology 2016, 178, (8), 1510-1521.
27. Yang, H.; Yu, H.; Shen, Z., A novel high-throughput and quantitative method based on visible color shifts for screening Bacillus subtilis THY-15 for surfactin production. Journal of Industrial Microbiology & Biotechnology 2015, 42, (8), 1139-1147.
28. Huan, Y.; Xu, L.; Xue, L.; Huimin, Y.; Zhongyao, S. J. A.; Chemistry, B., Identification of lipopeptide isoforms by MALDI-TOF-MS/MS based on the simultaneous purification of iturin, fengycin, and surfactin by RP-HPLC. 2015, 407, (9), 2529-2542.
29. Li, X.; Yang, H.; Zhang, D.; Li, X.; Yu, H.; Shen, Z., Overexpression of specific proton motive force-dependent transporters facilitate the export of surfactin in Bacillus subtilis. Journal of Industrial Microbiology & Biotechnology 2015, 42, (1), 93-103.
30. He, H.; Wei, Y.; Luo, H.; Li, X.; Wang, X.; Liang, C.; Chang, Y.; Yu, H.; Shen, Z., Immobilization and Stabilization of Cephalosporin C Acylase on Aminated Support by Crosslinking with Glutaraldehyde and Further Modifying with Aminated Macromolecules. Biotechnology Progress 2015, 31, (2), 387-395.
31. Luo, H.; Zhao, H.; Chang, Y.; Wang, Q.; Yu, H.; Shen, Z., Oriented Immobilization and Characterization of a Poly-Lysine-Tagged Cephalosporin C Acylase on Glyoxyl Agarose Support. Applied Biochemistry and Biotechnology 2015, 175, (4), 2114-2123.
32. Li, J.; Liu, J.; Chen, J.; Wang, Y.; Luo, G.; Yu, H., Multiple reuses of Rhodococcus ruber TH3 free cells to produce acrylamide in a membrane dispersion microreactor. Bioresource Technology 2015, 187, 198-204.
33. Li, J.; Yang, L.; Ding, X.; Chen, J.; Wang, Y.; Luo, G.; Yu, H., Visual study of mass transfer characterization in the process of biological catalytic hydration of acrylonitrile using pendant drop method. Rsc Advances 2015, 5, (96), 79164-79171.
34. Li, J.; Chen, J.; Wang, Y.; Luo, G.; Yu, H., Hydration of acrylonitrile to produce acrylamide using biocatalyst in a membrane dispersion microreactor. Bioresource Technology 2014, 169, 416-420.
35. Chen, J.; Jia, X.; Yu, H.; Luo, H.; Shen, Z., Catalytic kinetics of recombinant nitrile hydratase coupling terminal salt bridge and point-mutation. CIESC Journal 2014, 65, (7), 2821-2828.
36. Zhang, J.; Yu, H.; Wang, Y.; Luo, H.; Shen, Z. J. J. o. B., Determination of the second autoproteolytic cleavage site of cephalosporin C acylase and the effect of deleting its flanking residues in the α-C-terminal region. 2014, 184, (6), 138-145.
37. Shuai, Z.; Nakano, K.; Yu, H.; Shen, Z. J. M. R. E., Bio-nano complexes of ZVFeNPs/Fe-s-M13 and Cd (II)/Cd-s-M13 accelerate Cd (II) reduction by FeNPs through dual dispersing and separate deposition. 2014, 1, (1), 015043.
38. Chen, J.; Yu, H.; Liu, C.; Liu, J.; Shen, Z., Improving stability of nitrile hydratase by bridging the salt-bridges in specific thermal-sensitive regions. Journal of Biotechnology 2013, 164, (2), 354-362.
39. Zhang, J.; Wang, Z.-T.; Yu, H.-M.; Ma, Y., Paenibacillus catalpae sp nov., isolated from the rhizosphere soil of Catalpa speciosa. International Journal of Systematic and Evolutionary Microbiology 2013, 63, 1776-1781.
40. Cheng, F.; Tang, C.; Yang, H.; Yu, H.; Chen, Y.; Shen, Z., Characterization of a Blend-Biosurfactant of Glycolipid and Lipopeptide Produced by Bacillus subtilis TU2 Isolated from Underground Oil-Extraction Wastewater. Journal of Microbiology and Biotechnology 2013, 23, (3), 390-396.
41. Ma, Y.; Yu, H., Engineering of Rhodococcus cell catalysts for tolerance improvement by sigma factor mutation and active plasmid partition. Journal of Industrial Microbiology & Biotechnology 2012, 39, (10), 1421-1430.
42. Jian, Z.; Yuchao, M.; Huimin, Y. J. I. J. S. E. M., Arthrobacter cupressi sp. nov., an actinomycete isolated from the rhizosphere soil of Cupressus sempervirens. 2012, 62, (Pt 11), 2731-2736.
43. Jian, Z.; Ma, Y.; Yu, H. J. I. J. o. S.; Microbiology, E., Nocardioides lianchengensis sp. nov., a novel actinomycete isolated from soil of Liancheng county of Fujian province, China. 2012.
44. Wang, Y.; Yu, H.; Zhang, J.; Luo, H.; Shen, Z., Double knockout of beta-lactamase and cephalosporin acetyl esterase genes from Escherichia coli reduces cephalosporin C decomposition. Journal of Bioscience and Bioengineering 2012, 113, (6), 737-741.
45. Wang, Y.; Yu, H.; Song, W.; An, M.; Zhang, J.; Luo, H.; Shen, Z., Overexpression of synthesized cephalosporin C acylase containing mutations in the substrate transport tunnel. Journal of Bioscience and Bioengineering 2012, 113, (1), 36-41.
46. Zhu, X.; Luo, H.; Chang, Y.; Su, H.; Li, Q.; Yu, H.; Shen, Z., Characteristic of immobilized cephalosporin C acylase and its application in one-step enzymatic conversion of cephalosporin C to 7-aminocephalosporanic acid. World Journal of Microbiology & Biotechnology 2011, 27, (4), 823-829.
47. Sun, Y.; Yu, H.; Sun, X.; Shen, Z., Bi-steady state reaction kinetics of nitrile hydratase in free resting cells. Journal of Chemical Industry and Engineering (China) 2010, 61, (7), 1783-1789.
48. Yu, H.; Ma, Y., Gene knockout strategies for metabolic pathway regulation in industrial microbes. Sheng wu gong cheng xue bao = Chinese journal of biotechnology 2010, 26, (9), 1199-208.
49. Cheng, W. E. N.; Hui-min, Y. U.; Yun-peng, S. U. N.; Ying, W.; Zhong-yao, S., Efficient Quantification of Hyaluronic Acid in Fermentation Broth by Modified CTAB Method. Journal of Chinese Biotechnology 2010, 30, (2), 89-93.
50. Luo, H.; Fan, L.; Chang, Y.; Ma, J.; Yu, H.; Shen, Z., Gene Cloning, Overexpression, and Characterization of the Nitrilase from Rhodococcus rhodochrous tg1-A6 in E. coli. Applied Biochemistry and Biotechnology 2010, 160, (2), 393-400.
51. Ma, Y.; Yu, H.; Pan, W.; Liu, C.; Zhang, S.; Shen, Z., Identification of nitrile hydratase-producing Rhodococcus ruber TH and characterization of an amiE-negative mutant. Bioresource Technology 2010, 101, (1), 285-291.
52. Sun, X.; Yu, H.; Shen, Z., Deactivation Kinetics of Nitrile Hydratase in Free Resting Cells. Chinese Journal of Chemical Engineering 2009, 17, (5), 822-828.
53. Liu, C.; Yu, H.; Yuchao, M.; Pan, W.; Luo, H.; Shen, Z., Promoter recognition and beta-galactosidase reporter gene expression in Rhodococcus. Sheng wu gong cheng xue bao = Chinese journal of biotechnology 2009, 25, (9), 1360-5.
54. Ma, X.-F.; Yu, H.-M.; Wen, C.; Luo, H.; Li, Q.; Shen, Z.-Y., Triple fusion of d-amino acid oxidase from Trigonopsis variabilis with polyhistidine and Vitreoscilla hemoglobin. World Journal of Microbiology & Biotechnology 2009, 25, (8), 1353-1361.
55. Ling, T.; Zhu, J.; Yu, H.; Xie, L., Size Effect on Crystal Morphology of Faceted Face-Centered Cubic Fe Nanoparticles. Journal of Physical Chemistry C 2009, 113, (22), 9450-9453.
56. Klein-Marcuschamer, D.; Santos, C. N. S.; Yu, H.; Stephanopoulos, G., Mutagenesis of the Bacterial RNA Polymerase Alpha Subunit for Improvement of Complex Phenotypes. Applied and Environmental Microbiology 2009, 75, (9), 2705-2711.
57. Ling, T.; Xie, L.; Zhu, J.; Yu, H.; Ye, H.; Yu, R.; Cheng, Z.; Liu, L.; Liu, L.; Yang, G.; Cheng, Z.; Wang, Y.; Ma, X., Icosahedral Face-Centered Cubic Fe Nanoparticles: Facile Synthesis and Characterization with Aberration-Corrected TEM. Nano Letters 2009, 9, (4), 1572-1576.