Directed evolution of 3-phosphoglycerate dehydrogenase from Corynebacterium glutamicum

  • HUANG Xinyan ,
  • SUN Mujiao ,
  • DU Muhua ,
  • PAN Yue ,
  • ZHANG Xinyu ,
  • ZHANG Yaohan ,
  • XU Ning ,
  • LIU Jun ,
  • JU Jiansong ,
  • WEI Liang
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  • 1(College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China)
    2(Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China)
    3(College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China)
    4(College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China)

Received date: 2024-02-01

  Revised date: 2024-04-02

  Online published: 2025-02-21

Abstract

3-Phosphoglycerate dehydrogenase (PGDH) is the rate-limiting enzyme in the biosynthetic pathway of L-serine, playing a crucial role in efficient L-serine synthesis.In this study, the enzymatic characteristics of PGDH from Corynebacterium.glutamicum was investigated.The results indicated that the enzyme activity of Cg-PGDH was only 1.98 U/mg with poor thermal stability, which significantly hindered the high-efficiency biosynthesis of L-serine.To address this issue, directed evolution and high-throughput screening were employed to enhance the catalytic activity and thermal stability of Cg-PGDH.Through multiple rounds of screening, five mutants with significantly improved catalytic activity were obtained, including P85Q, D365Y, A389T, A183V, and I231V.Notably, the P85Q mutant exhibited a 1.55-fold increase in enzyme activity and significantly improved temperature stability, demonstrating an optimum catalytic temperature of 60 ℃.Subsequently, the combined mutations on the mutation sites of five mutants including P85Q, D365Y, A389T, A183V, and I231V were conducted, leading to the mutant P85Q-D365Y with enhanced temperature stability.Structural analysis and molecular dynamics simulations of the mutated sites within Cg-PGDH revealed that, despite P85Q and D365Y not being located in the catalytic center, they enhanced the stability of the loop in the 130-140 region, thereby increasing substrate affinity and catalytic activity.These research findings provided a significant foundation and direction for further elucidating the catalytic mechanism of Cg-PGDH and enhancing its catalytic activity.

Cite this article

HUANG Xinyan , SUN Mujiao , DU Muhua , PAN Yue , ZHANG Xinyu , ZHANG Yaohan , XU Ning , LIU Jun , JU Jiansong , WEI Liang . Directed evolution of 3-phosphoglycerate dehydrogenase from Corynebacterium glutamicum[J]. Food and Fermentation Industries, 2025 , 51(3) : 89 -96 . DOI: 10.13995/j.cnki.11-1802/ts.038795

References

[1] MITSUHASHI S.Current topics in the biotechnological production of essential amino acids, functional amino acids, and dipeptides[J].Current Opinion in Biotechnology, 2014, 26:38-44.
[2] 卢发, 张伟国.L-丝氨酸产生菌的分离筛选及发酵条件[J].食品与生物技术学报, 2005, 24(2):46-49; 54.
LU F, ZHANG W G.Screening of L-serine producer and the fermentation conditions in shake-flask culture[J].Journal of Food Science and Biotechnology, 2005, 24(2):46-49; 54.
[3] EAGLE H.Amino acid metabolism in mammalian cell cultures[J].Science, 1959, 130(3373):432-437.
[4] FAN W, TANG S, FAN X J, et al.SIRT1 regulates sphingolipid metabolism and neural differentiation of mouse embryonic stem cells through c-Myc-SMPDL3B[J].eLife, 2021, 10:e67452.
[5] PHONE MYINT S M M, SUN L Y.L-serine:Neurological implications and therapeutic potential[J].Biomedicines, 2023, 11(8):2117.
[6] 杨帆. 利用重组大肠杆菌生产L-丝氨酸的研究[D].济南:山东大学, 2013.
YANG F.Production of L-serine in recombinant Escherichia coli[D].Jinan:Shandong University, 2013.
[7] 克丽凤, 张伟国, 钱和.L-丝氨酸的生产及其应用[J].江苏食品与发酵, 2001(2):19-22.
KE L F, ZHANG W G, QIAN H.Production and application of L-serine[J].Jiangsu Food and Fermentation, 2001(2):19-22.
[8] EFFENBERGER F, ZOLLER G.Amino acids;13 Investigations on the synthesis of dl-serine from α-haloacrylic acid derivatives[J].Tetrahedron, 1988, 44(17):5573-5582.
[9] ZHU G Y, ZHU X, WAN X L, et al.Hydrolysis technology and kinetics of poultry waste to produce amino acids in subcritical water[J].Journal of Analytical and Applied Pyrolysis, 2010, 88(2):187-191.
[10] JIANG W, XIA B Z, LIU Z D.A serine hydroxymethyltransferase from marine bacterium Shewanella algae:Isolation, purification, characterization and L-serine production[J].Microbiological Research, 2013, 168(8):477-484.
[11] 朱林江, 李崎.L-丝氨酸的微生物法制备研究进展[J].食品与发酵工业, 2015, 41(1):181-185.
ZHU L J, LI Q.Microbial production of L-serine[J].Food and Fermentation Industries, 2015, 41(1):181-185.
[12] XU G Q, JIN X X, GUO W, et al.Characterization, modification, and overexpression of 3-phosphoglycerate dehydrogenase in Corynebacterium glutamicum for enhancing L-serine production[J].Annals of Microbiology, 2015, 65(2):929-935.
[13] BELL J K, PEASE P J, BELL J E, et al.De-regulation of D-3-phosphoglycerate dehydrogenase by domain removal[J].European Journal of Biochemistry, 2002, 269(17):4176-4184.
[14] GRANT G A.Transient kinetic analysis of L-serine interaction with Escherichia coli D-3-phosphoglycerate dehydrogenase containing amino acid mutations in the hinge regions[J].Biochemistry, 2011, 50(14):2900-2906.
[15] GRANT G A, XU X L, HU Z.Role of an interdomain Gly-Gly sequence at the regulatory-substrate domain interface in the regulation of Escherichia coli D-3-phosphoglycerate dehydrogenase[J].Biochemistry, 2000, 39(24):7316-7319.
[16] 金雪霞. 基因serA及sdaA对谷氨酸棒杆菌SYPS-062积累L-丝氨酸的影响分析[D].无锡:江南大学, 2011.
JIN X X.Effects of genes serA and sdaA on accumulation of L-serine in Corynebacterium glutamicum SYPS-062[D].Wuxi:Jiangnan University, 2011.
[17] 来书娟, 张芸, 刘树文, 等.产L-丝氨酸谷氨酸棒杆菌的代谢工程改造和代谢流分析[J].中国科学:生命科学, 2012, 42(4):295-303.
LAI S J, ZHANG Y, LIU S W, et al.Metabolic engineering and metabolic flux analysis of L-serine-producing Corynebacterium glutamicum[J].Scientia Sinica (Vitae), 2012, 42(4):295-303.
[18] PETERS-WENDISCH P, NETZER R, EGGELING L, et al.3-phosphoglycerate dehydrogenase from Corynebacterium glutamicum:The C-terminal domain is not essential for activity but is required for inhibition by L-serine[J].Applied Microbiology and Biotechnology, 2002, 60(4):437-441.
[19] 邓辉, 陈存武, 孙传伯, 等.大肠杆菌磷酸甘油酸脱氢酶突变体的构建及抗反馈抑制效应[J].生物工程学报, 2016, 32(4):468-477.
DENG H, CHEN C W, SUN A, et al.Construction and characterization of Escherichia coli D-3-phosphoglycerate dehydrogenase mutants with feedback-inhibition relief[J].Chinese Journal of Biotechnology, 2016, 32(4):468-477.
[20] SINGH R K, RAJ I, PUJARI R, et al.Crystal structures and kinetics of Type III 3-phosphoglycerate dehydrogenase reveal catalysis by lysine[J].The FEBS Journal, 2014, 281(24):5498-5512.
[21] 周翠燕, 俞敏达, 李文奇.三种测定蛋白质热稳定性方法的比较[J].分析测试技术与仪器, 2021, 27(4):252-259.
ZHOU C Y, YU M D, LI W Q.Comparation of three measuring methods for thermodynamic stability of protein[J].Analysis and Testing Technology and Instruments, 2021, 27(4):252-259.
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