Advertisement

Applied Microbiology and Biotechnology

, Volume 103, Issue 21–22, pp 8839–8851 | Cite as

Biocatalytic production of D-p-hydroxyphenylglycine by optimizing protein expression and cell wall engineering in Escherichia coli

  • Yang Liu
  • Lingfeng Zhu
  • Wenpeng Qi
  • Bo YuEmail author
Biotechnological products and process engineering

Abstract

D-p-hydroxyphenylglycine (D-HPG) functions as an intermediate and has important value in antibiotic industries. The high pollution and costs from chemical processes make biotechnological route for D-HPG highly desirable. Here, a whole-cell transformation process by D-hydantoinase(Hase) and D-carbamoylase(Case) was developed to produce D-HPG from DL-hydroxyphenylhydantoin(DL-HPH) in Escherichia coli. The artificially designed ribosome binding site with strong intensity significantly facilitated the protein expression of limiting step enzyme Case. Next, the cell wall permeability was improved by disturbing the peptidoglycan structure by overproduction of D,D-carboxypeptidases without obviously affecting cell growth, to increase the bioavailability of low soluble hydantoin substrate. By fine-tuning regulation of expression level of D,D-carboxypeptidase DacB, the final production yield of D-HPG increased to 100% with 140 mM DL-HPH substrate under the optimized transformation conditions. This is the first example to enhance bio-productivity of chemicals by cell wall engineering and creates a new vision on biotransformation of sparingly soluble substrates. Additionally, the newly demonstrated ‘hydroxyl occupancy’ phenomenon when Case reacts with hydroxyl substrates provides a referential information for the enzyme engineering in future.

Keywords

D-p-hydroxyphenylglycine Cell permeability D,D-carboxypeptidase D-carbamoylase Escherichia coli 

Notes

Funding information

The work was supported by Beijing Natural Science Foundation, China (5182021), National Science Foundation of China (11604359), and Ministry of Science & Technology, China (KY201701011).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interests.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

References

  1. Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, Lindahl E (2015) GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1-2:19–25Google Scholar
  2. Andreas SB, Michael S, Karlheinz D (1998) Biocatalysis to amino acid-based chiral pharmaceuticals-examples and perspectives. J Mol Catal B-Enzym 5(1-4):1–11Google Scholar
  3. Beveridge TJ (1999) Structures of gram-negative cell walls and their derived membrane vesicles. J Bacteriol 181(16):4725–4733PubMedPubMedCentralGoogle Scholar
  4. Cai YH, Trodler P, Jiang S, Zhang W, Wu Y, Lu YH, Yang S, Jiang WH (2009) Isolation and molecular characterization of a novel D-hydantoinase from Jannaschia sp. CCS1. FEBS J 276(13):3575–3588PubMedGoogle Scholar
  5. Cescau S, Debarbieux L, Wandersman C (2007) Probing the in vivo dynamics of Type I protein secretion complex association through sensitivity to detergents. J Bacteriol 189(5):1496–1504PubMedGoogle Scholar
  6. Chao YP, Fu H, Lo TE, Chen PT, Wang JJ (1999)One-step production of D-p-hydroxyphenylglycine by recombinant Escherichia coli strains. Biotechnol Prog 15(6):1039–1045PubMedGoogle Scholar
  7. Chen XY, Zaro JL, Shen WC (2013) Fusion protein linkers: property, design and functionality. Adv Drug Deliv Rev 65(10):1357–1369PubMedGoogle Scholar
  8. Cheon YH, Kim HS, Han KH, Abendroth J, Niefind K, Schomburg D, Wang J, Kim Y (2002) Crystal structure of D-hydantoinase from Bacillus stearothermophilus: insight into the stereochemistry of enantioselectivity. Biochemistry 41(30):9410–9417PubMedGoogle Scholar
  9. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N•log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092Google Scholar
  10. Denome SA, Elf PK, Henderson TA, Nelson DE, Young KD (1999)Escherichia coli mutants lacking all possible combinations of eight penicillin binding proteins: viability, characteristics, and implications for peptidoglycan synthesis. J Bacteriol 181(13):3981–3993PubMedPubMedCentralGoogle Scholar
  11. Fan CH, Lee CK, Chao YP (2000) Recombinant Escherichia coli cell for D-p-hydroxyphenylglycine production from D-N-carbamoyl-p- hydroxyphenylglycine. Enzym Microb Technol 26(2-4):222–228Google Scholar
  12. Horne D, Hakenbeck R, Tomasz A (1977) Secretion of lipids induced by inhibition of peptidoglycan synthesis in streptococci. J Bacteriol 132(2):704–717PubMedPubMedCentralGoogle Scholar
  13. Ikenaka Y, Nanba H, Yamada Y, Yajima K, Takano M, Takahashi S (1998) Screening, characterization, and cloning of the gene for N-carbamyl-D-amino acid amidohydrolase from thermotolerant soil bacteria. Biosci Biotechnol Biochem 62(5):882–886PubMedGoogle Scholar
  14. Jiang S, Li CH, Zhang WW, Cai YH, Yang YL, Yang S, Jiang WH (2007) Directed evolution and structural analysis of N-carbamoyl-D-amino acid amidohydrolase provide insights into recombinant protein solubility in Escherichia coli. Biochem J 402(3):429–437PubMedPubMedCentralGoogle Scholar
  15. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935Google Scholar
  16. Kim GJ, Kim HS (1995) Optimization of the enzymatic synthesis of D-p-hydroxyphenylglycine from DL-5-substituted hydantoin using D-hydantoinase and N-carbamoylase. Enzym Microb Technol 17(1):63–67Google Scholar
  17. Kishida H, Unzai S, Roper DI, Lloyd A, Park SY, Tame JR (2006) Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics. Biochemistry 45(3):783–792PubMedGoogle Scholar
  18. Lapointe G, Leblanc D, Morin A (1995) Use of a polymerase-chain-reaction-amplified DNA probe from Pseudomonas putida to detect D-hydantoinase-producing microorganisms by direct colony hybridization. Appl Microbiol Biotechnol 42(6):895–900PubMedGoogle Scholar
  19. Lee DC, Kim HS (1998) Optimization of a heterogeneous reaction system for the production of optically active D-amino acids using thermostable D-hydantoinase. Biotechnol Bioeng 60(6):729–738PubMedGoogle Scholar
  20. Lee SG, Lee DC, Hong SP, Sung MH, Kim HS (1995) Thermostable D-hydantoinase from thermophilic Bacillus stearothermophilus SD-1: characteristics of purified enzyme. Appl Microbiol Biotechnol 43(2):270–276Google Scholar
  21. Lehrer RI, Barton A, Ganz T (1988) Concurrent assessment of inner and outer membrane permeabilization and bacteriolysis in E. coli by multiple-wavelength spectrophotometry. J Immunol Methods 108(1-2):153–158PubMedGoogle Scholar
  22. Liu YQ, Li Q, Hu XJ, Yang JC (2008) Construction and co-expression of polycistronic plasmid encoding D-hydantoinase and D-carbamoylase for the production of D-amino acids. Enzym Microb Technol 42(7):589–593Google Scholar
  23. Liu YF, Xu GC, Han RZ, Dong JJ, Ni Y (2017) Identification of D-carbamoylase for biocatalytic cascade synthesis of D-tryptophan featuring high enantioselectivity. Bioresour Technol 249:720–728PubMedGoogle Scholar
  24. Liu B, Xiang SM, Zhao G, Wang BJ, Ma YH, Liu WF, Tao Y (2019) Efficient production of 3-hydroxypropionate from fatty acids feedstock in Escherichia coli. Metab Eng 51:121–130PubMedGoogle Scholar
  25. Loh B, Grant C, Hancock RE (1984) Use of the fluorescent probe 1-N-phenylnaphthylamine to study the interactions of aminoglycoside antibiotics with the outer membrane of Pseudomonas aeruginosa. Antimicrob Agents Chemother 26(4):546–551PubMedPubMedCentralGoogle Scholar
  26. Louwrier A, Knowles CJ (1996) The purification and characterization of a novel D-specific carbamoylase enzyme from an Agrobacterium sp. Enzym Microb Technol 19(8):562–571Google Scholar
  27. Mengin-Lecreulx D, Lemaitre B (2005) Structure and metabolism of peptidoglycan and molecular requirements allowing its detection by the Drosophila innate immune system. J Endotoxin Res 11(2):105–111PubMedGoogle Scholar
  28. Möller A, Syldatk C, Schulze M, Wagner F (1988)Stereo- and substrate-specificity of a D-hydantoinase and a D-N-carbamyl-amino acid amidohydrolase of Arthrobacter crystallopoietes AM 2. Enzym Microb Technol 10(10):618–625Google Scholar
  29. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J Comput Chem 30(16):2785–2791PubMedPubMedCentralGoogle Scholar
  30. Nakai T, Hasegawa T, Yamashita E, Yamamoto M, Kumasaka T, Ueki T, Nanba H, Ikenaka Y, Takahashi S, Sato M, Tsukihara T (2000) Crystal structure of N-carbamyl-D-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases. Structure 8(7):729–739PubMedGoogle Scholar
  31. Nanba H, Ikenaka Y, Yamada Y, Yajima K, Takano M, Takahashi S (1998) Isolation of Agrobacterium sp. strain KNK712 that produces N-carbamyl-D-amino acid amidohydrolase, cloning of the gene for this enzyme, and properties of the enzyme. Biosci Biotechnol Biochem 62(5):875–881PubMedGoogle Scholar
  32. Nandanwar H, Prajapati R, Hoondal GS (2013) (D)-p-Hydroxyphenylglycine production by thermostable D-hydantoinase from Brevibacillus parabrevis-PHG1. Biocatal Biotransform 31(1):22–32Google Scholar
  33. Nanninga N (1998) Morphogenesis of Escherichia coli. Microbiol Mol Biol Rev 62(1):110–129PubMedPubMedCentralGoogle Scholar
  34. Nelson DE, Young KD (2001) Contributions of PBP 5 and D,D-carboxypeptidase penicillin binding proteins to maintenance of cell shape in Escherichia coli. J Bacteriol 183(10):3055–3064PubMedPubMedCentralGoogle Scholar
  35. Nose S (1984) A unified formulation of the constant temperature molecular-dynamics methods. J Chem Phys 81:511–519Google Scholar
  36. Nowroozi FF, Baidoo EE, Ermakov S, Redding-Johanson AM, Batth TS, Petzold CJ, Keasling JD (2014) Metabolic pathway optimization using ribosome binding site variants and combinatorial gene assembly. Appl Microbiol Biotechnol 98(4):1567–1581PubMedGoogle Scholar
  37. Ogawa J, Shimizu S, Yamada H (1993)N-carbamoyl-D-amino acid amidohydrolase from Comamonas sp. E222c purification and characterization. Eur J Biochem 212(3):685–691PubMedGoogle Scholar
  38. Olivieri R, Fascetti E, Angelini L, Degen L (1979) Enzymatic conversion of N- carbamoyl-D-amino acids to D-amino acids. Enzym Microb Technol 1(3):201–204Google Scholar
  39. Olivieri R, Fascetti E, Angelini L, Degen L (1981) Microbial transformation of racemic hydantoins to D-amino acids. Biotechnol Bioeng 23(10):2173–2183Google Scholar
  40. Park JH, Kim GJ, Lee SG, Kim HS (1998) Biochemical properties of thermostable D-hydantoinase from Bacillus thermocatenulatus GH-2. Ann N Y Acad Sci 864(1):337–340PubMedGoogle Scholar
  41. Park JH, Kim GJ, Kim HS (2000) Production of D-amino acid using whole cells of recombinant Escherichia coli with separately and coexpressed D-hydantoinase and N-carbamoylase. Biotechnol Prog 16(4):564–570PubMedGoogle Scholar
  42. Parrinello M, Rahman A (1981) Polymorphic transitions in single-crystals - a new molecular-dynamics method. J Appl Physiol 52:7182–7190Google Scholar
  43. Qian JQ, Chen CC, Liu M, Lv BF (2012) Bioconversion production D-p-hydrophenyglycine from DL-p-hydroxyphenylhydantoin by Pseudomonas putida in aqueous two-phase system. Indian J Biotechnol 11:445–452Google Scholar
  44. Runser SM, Meyer PC (1993) Purification and biochemical characterization of the hydantoin hydrolyzing enzyme from Agrobacterium species. A hydantoinase with no 5,6-dihydropyrimidine amidohydrolase activity. Eur J Biochem 213(3):1315–1324PubMedGoogle Scholar
  45. Schüttelkopf AW, van Aalten DM (2004) PRODRG - a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D60:1355–1363Google Scholar
  46. Sorin EJ, Pande VS (2005) Exploring the Helix-Coil transition via all-atom equilibrium ensemble simulations. Biophys J 88(4):2472–2493PubMedPubMedCentralGoogle Scholar
  47. Typas A, Banzhaf M, Gross CA, Vollmer W (2011) From the regulation of peptidoglycan synthesis to bacterial growth and morphology. Nat Rev Microbiol 10(2):123–136PubMedPubMedCentralGoogle Scholar
  48. Vollmer W, Blanot D, de Pedro MA (2008) Peptidoglycan structure and architecture. FEMS Microbiol Rev 32(2):149–167PubMedGoogle Scholar
  49. Wu S, Liu Y, Liu YB, Zhao GG, Wang JJ, Sun WR (2005) Enzymatic production of D-p-hydroxyphenylglycine from DL-5-p-hydroxyphenylhydantoin by Sinorhizobium morelens S-5. Enzym Microb Technol 36(4):520–526Google Scholar
  50. Wu H, Chen J, Chen GQ (2016) Engineering the growth pattern and cell morphology for enhanced PHB production by Escherichia coli. Appl Microbiol Biotechnol 100(23):9907–9916PubMedGoogle Scholar
  51. Xu Z, Liu YQ, Yang YL, Jiang WH, Arnold E, Ding JP (2003) Crystal structure of D-hydantoinase from Burkholderia pickettii at a resolution of 2.7 Angstroms: insights into the molecular basis of enzyme thermostability. J Bacteriol 185(14):4038–4049PubMedPubMedCentralGoogle Scholar
  52. Yang HQ, Lu X, Hu JY, Chen Y, Shen W, Liu L (2018a) Boosting secretion of extracellular protein by Escherichia coli via cell wall perturbation. Appl Environ Microbiol 84(20):e01382–e01318PubMedPubMedCentralGoogle Scholar
  53. Yang HQ, Hu JY, Lu X, Wang FX, Shen W, Hu W, Wang LL, Chen XZ, Liu L (2018b) Improving extracellular protein production in Escherichia coli by overexpressing D,D-carboxypeptidase to perturb peptidoglycan network synthesis and structure. Appl Microbiol Biotechnol 103(2):793–806PubMedGoogle Scholar
  54. Yu H, Yang S, Jiang W, Yang Y (2009) Efficient biocatalytic production of D-4-hydroxyphenylglycine by whole cells of recombinant Ralstonia pickettii. Folia Microbiol 54(6):509–515Google Scholar
  55. Zhang DL, Zhu FY, Fan WC, Tao RS, Yu H, Yang YL, Jiang WH, Yang S (2011) Gradually accumulating beneficial mutations to improve the thermostability of N-carbamoyl-d-amino acid amidohydrolase by step-wise evolution. Appl Microbiol Biotechnol 90(4):1361–1371PubMedGoogle Scholar
  56. Zhang SS, Zhao XJ, Tao Y, Lou CB (2015) A novel approach for metabolic pathway optimization: Oligo-linker mediated assembly (OLMA) method. J Biol Eng 9:23PubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
  2. 2.University of Chinese Academy of SciencesBeijingChina
  3. 3.IBG-1: Biotechnology, Institute of Bio- and GeosciencesForschungszentrum JülichJülichGermany
  4. 4.Shanghai Institute of Applied PhysicsChinese Academy of SciencesShanghaiChina
  5. 5.China-Thailand Joint Laboratory on Microbial BiotechnologyBeijingChina

Personalised recommendations