Skip to main content

Biomanufacturing by In Vitro Biotransformation (ivBT) Using Purified Cascade Multi-enzymes

  • Chapter
  • First Online:
Cell-free Production

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 186))

  • 344 Accesses

Abstract

In vitro biotransformation (ivBT) refers to the use of an artificial biological reaction system that employs purified enzymes for the one-pot conversion of low-cost materials into biocommodities such as ethanol, organic acids, and amino acids. Unshackled from cell growth and metabolism, ivBT exhibits distinct advantages compared with metabolic engineering, including but not limited to high engineering flexibility, ease of operation, fast reaction rate, high product yields, and good scalability. These characteristics position ivBT as a promising next-generation biomanufacturing platform. Nevertheless, challenges persist in the enhancement of bulk enzyme preparation methods, the acquisition of enzymes with superior catalytic properties, and the development of sophisticated approaches for pathway design and system optimization. In alignment with the workflow of ivBT development, this chapter presents a systematic introduction to pathway design, enzyme mining and engineering, system construction, and system optimization. The chapter also proffers perspectives on ivBT development.

Graphical Abstract

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 219.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 279.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Zhang Y-HP, Sun J, Ma Y (2017) Biomanufacturing: history and perspective. J Ind Microbiol Biotechnol 44(4–5):773–784. https://doi.org/10.1007/s10295-016-1863-2

    Article  CAS  PubMed  Google Scholar 

  2. Claassens NJ, Burgener S, Vogeli B, Erb TJ, Bar-Even A (2019) A critical comparison of cellular and cell-free bioproduction systems. Curr Opin Biotechnol 60:221–229. https://doi.org/10.1016/j.copbio.2019.05.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Buchner E (1897) Alkoholische Gärung ohne Hefezellen. Ber Dtsch Chem Ges 30:117–124

    Article  CAS  Google Scholar 

  4. Fernandes P (2010) Enzymes in food processing: a condensed overview on strategies for better biocatalysts. Enzyme Res 2010:862537. https://doi.org/10.4061/2010/862537

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Bornscheuer UT, Huisman GW, Kazlauskas RJ, Lutz S, Moore JC, Robins K (2012) Engineering the third wave of biocatalysis. Nature 485(7397):185–194. https://doi.org/10.1038/nature11117

    Article  CAS  PubMed  Google Scholar 

  6. Fessner WD (2015) Systems biocatalysis: development and engineering of cell-free “artificial metabolisms” for preparative multi-enzymatic synthesis. New Biotechnol 32(6):658–664. https://doi.org/10.1016/j.nbt.2014.11.007

    Article  CAS  Google Scholar 

  7. Melinek B, Colant N, Stamatis C, Lennon C, Farid S, Polizzi K et al (2020) Toward a roadmap for cell-free synthesis in bioprocessing. BioProcess Int. https://doi.org/10.1016/B978-0-08-100623-8.00044-X

  8. Pe’ery T, Mathews MB (1997) Synthesis and purification of single-stranded RNA for use in experiments with PKR and in cell-free translation systems. Methods 11(4):371–381. https://doi.org/10.1006/meth.1996.0435

    Article  PubMed  Google Scholar 

  9. Pardee K, Slomovic S, Nguyen PQ, Lee JW, Donghia N, Burrill D et al (2016) Portable, on-demand biomolecular manufacturing. Cell 167(1):248–259.e12. https://doi.org/10.1016/j.cell.2016.09.013

    Article  CAS  PubMed  Google Scholar 

  10. Stamatis C, Farid SS (2021) Process economics evaluation of cell-free synthesis for the commercial manufacture of antibody drug conjugates. Biotechnol J 16(4):e2000238. https://doi.org/10.1002/biot.202000238

    Article  CAS  PubMed  Google Scholar 

  11. Zhang Y-HP (2010) Production of biocommodities and bioelectricity by cell-free synthetic enzymatic pathway biotransformations: challenges and opportunities. Biotechnol Bioeng 105(4):663–677. https://doi.org/10.1002/bit.22630

    Article  CAS  PubMed  Google Scholar 

  12. Zhu Z, You C, Ma Y, Zhang Y-HPJ (2018) In vitro synthetic enzymatic biosystems at the interface of the food-energy-water nexus: a conceptual framework and recent advances. Process Biochem 74:43–49. https://doi.org/10.1016/j.procbio.2018.07.002

    Article  CAS  Google Scholar 

  13. Zhu Z, Kin Tam T, Sun F, You C, Zhang Y-HP (2014) A high-energy-density sugar biobattery based on a synthetic enzymatic pathway. Nat Commun 5:3026. https://doi.org/10.1038/ncomms4026

    Article  CAS  PubMed  Google Scholar 

  14. Zhu Z, Zhang Y-HP (2017) In vitro metabolic engineering of bioelectricity generation by the complete oxidation of glucose. Metab Eng 39:110–116. https://doi.org/10.1016/j.ymben.2016.11.002

    Article  CAS  PubMed  Google Scholar 

  15. Wu R, Li F, Cui X, Li Z, Ma C, Jiang H et al (2023) Enzymatic electrosynthesis of glycine from CO2 and NH3. Angew Chem Int Ed Engl. https://doi.org/10.1002/ange.202218387

  16. Li F, Wei X, Zhang L, Liu C, You C, Zhu Z (2022) Installing a green engine to drive an enzyme cascade: a light-powered in vitro biosystem for poly(3-hydroxybutyrate) synthesis. Angew Chem Int Ed Engl 61:e202111054. https://doi.org/10.1002/anie.202111054

    Article  CAS  PubMed  Google Scholar 

  17. Rollin JA, Tam TK, Zhang Y-HP (2013) New biotechnology paradigm: cell-free biosystems for biomanufacturing. Green Chem 15(7):1708–1719. https://doi.org/10.1039/C3GC40625C

    Article  CAS  Google Scholar 

  18. Sun S, Wei X, You C (2019) The construction of an in vitro synthetic enzymatic biosystem that facilitates laminaribiose biosynthesis from maltodextrin and glucose. Biotechnol J 14(4):e1800493. https://doi.org/10.1002/biot.201800493

    Article  CAS  PubMed  Google Scholar 

  19. Li Y, Shi T, Han P, You C (2021) Thermodynamics-driven production of value-added D-allulose from inexpensive starch by an in vitro enzymatic synthetic biosystem. ACS Catal 11(9):5088–5099. https://doi.org/10.1021/acscatal.0c05718

    Article  CAS  Google Scholar 

  20. Sun S, Wei X, Zhou X, You C (2021) Construction of an artificial in vitro synthetic enzymatic platform for upgrading low-cost starch to value-added disaccharides. J Agric Food Chem 69(1):302–314. https://doi.org/10.1021/acs.jafc.0c06936

    Article  CAS  PubMed  Google Scholar 

  21. You C, Shi T, Li YJ, Han PP, Zhou XG, Zhang Y-HP (2017) An in vitro synthetic biology platform for the industrial biomanufacturing of myo-inositol from starch. Biotechnol Bioeng 114(8):1855–1864. https://doi.org/10.1002/bit.26314

    Article  CAS  PubMed  Google Scholar 

  22. Meng D, Wei X, Zhang Y-HPJ, Zhu Z, You C, Ma Y (2018) Stoichiometric conversion of cellulosic biomass by in vitro synthetic enzymatic biosystems for biomanufacturing. ACS Catal 8(10):9550–9559. https://doi.org/10.1021/acscatal.8b02473

    Article  CAS  Google Scholar 

  23. Wei X, Li Q, Hu C, You C (2021) An ATP-free in vitro synthetic enzymatic biosystem facilitating one-pot stoichiometric conversion of starch to mannitol. Appl Microbiol Biotechnol 105(5):1913–1924. https://doi.org/10.1007/s00253-021-11154-9

    Article  CAS  PubMed  Google Scholar 

  24. Schwander T, Schada von Borzyskowski L, Burgener S, Cortina NS, Erb TJ (2016) A synthetic pathway for the fixation of carbon dioxide in vitro. Science 354(6314):900–904. https://doi.org/10.1126/science.aah5237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Xie L, Wei X, Zhou X, Meng D, Zhou R, Zhang YPJ et al (2018) Conversion of D-glucose to L-lactate via pyruvate by an optimized cell-free enzymatic biosystem containing minimized reactions. Synth Syst Biotechnol 3(3):204–210. https://doi.org/10.1016/j.synbio.2018.05.003

    Article  PubMed  PubMed Central  Google Scholar 

  26. Shi T, Liu S, Zhang YPJ (2019) CO2 fixation for malate synthesis energized by starch via in vitro metabolic engineering. Metab Eng 55:152–160. https://doi.org/10.1016/j.ymben.2019.07.005

    Article  CAS  PubMed  Google Scholar 

  27. You C, Chen H, Myung S, Sathitsuksanoh N, Ma H, Zhang XZ et al (2013) Enzymatic transformation of nonfood biomass to starch. Proc Natl Acad Sci U S A 110(18):7182–7187. https://doi.org/10.1073/pnas.1302420110

    Article  PubMed  PubMed Central  Google Scholar 

  28. Opgenorth PH, Korman TP, Bowie JU (2016) A synthetic biochemistry module for production of bio-based chemicals from glucose. Nat Chem Biol 12(6):393–395. https://doi.org/10.1038/nchembio.2062

    Article  CAS  PubMed  Google Scholar 

  29. Li Q, Ma Z, Meng D, Sui X, You C (2021) Facile biosynthesis of synthetic crystalline cellulose nanoribbon from maltodextrin through a minimized two-enzyme phosphorylase cascade and its application in emulsion. J Biotechnol 332:54–60. https://doi.org/10.1016/j.jbiotec.2021.03.018

    Article  CAS  PubMed  Google Scholar 

  30. Meng D, Wei X, Bai X, Zhou W, You C (2020) Artificial in vitro synthetic enzymatic biosystem for the one-pot sustainable biomanufacturing of glucosamine from starch and inorganic ammonia. ACS Catal 10(23):13809–13819. https://doi.org/10.1021/acscatal.0c03767

    Article  CAS  Google Scholar 

  31. Zhu Z, Sun F, Zhang X, Zhang Y-HP (2012) Deep oxidation of glucose in enzymatic fuel cells through a synthetic enzymatic pathway containing a cascade of two thermostable dehydrogenases. Biosens Bioelectron 36(1):110–115. https://doi.org/10.1016/j.bios.2012.04.001

    Article  CAS  PubMed  Google Scholar 

  32. Wu R, Ma C, Zhang Y-HP, Zhu Z (2018) Complete oxidation of xylose for bioelectricity generation by reconstructing a bacterial xylose utilization pathway in vitro. ChemCatChem 10(9):2030–2035. https://doi.org/10.1002/cctc.201702018

    Article  CAS  Google Scholar 

  33. Myung S, Rollin J, You C, Sun F, Chandrayan S, Adams MW et al (2014) In vitro metabolic engineering of hydrogen production at theoretical yield from sucrose. Metab Eng 24:70–77. https://doi.org/10.1016/j.ymben.2014.05.006

    Article  CAS  PubMed  Google Scholar 

  34. Rollin JA, Martin del Campo J, Myung S, Sun F, You C, Bakovic A et al (2015) High-yield hydrogen production from biomass by in vitro metabolic engineering: mixed sugars coutilization and kinetic modeling. Proc Natl Acad Sci U S A 112(16):4964–4969. https://doi.org/10.1073/pnas.1417719112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Moustafa HMA, Kim EJ, Zhu ZG, Wu CH, Zaghloul TI, Adams MWW et al (2016) Water splitting for high-yield hydrogen production energized by biomass xylooligosaccharides catalyzed by an enzyme cocktail. ChemCatChem 8(18):2898–2902. https://doi.org/10.1002/cctc.201600772

    Article  CAS  Google Scholar 

  36. Kim EJ, Kim JE, Zhang Y-HPJ (2018) Ultra-rapid rates of water splitting for biohydrogen gas production through in vitro artificial enzymatic pathways. Energy. Environ Sci 11(8):2064–2072. https://doi.org/10.1039/C8EE00774H

    Article  CAS  Google Scholar 

  37. Wang W, Liu M, You C, Li Z, Zhang Y-HP (2017) ATP-free biosynthesis of a high-energy phosphate metabolite fructose 1,6-diphosphate by in vitro metabolic engineering. Metab Eng 42:168–174. https://doi.org/10.1016/j.ymben.2017.06.006

    Article  CAS  PubMed  Google Scholar 

  38. Wang W, Yang JG, Sun YX, Li ZM, You C (2020) Artificial ATP-free in vitro synthetic enzymatic biosystems facilitate aldolase-mediated C-C bond formation for biomanufacturing. ACS Catal 10(2):1264–1271. https://doi.org/10.1021/acscatal.9b04696

    Article  CAS  Google Scholar 

  39. Cai T, Sun H, Qiao J, Zhu L, Zhang F, Zhang J et al (2021) Cell-free chemoenzymatic starch synthesis from carbon dioxide. Science 373(6562):1523–1527. https://doi.org/10.1126/science.abh4049

    Article  CAS  PubMed  Google Scholar 

  40. Flamholz A, Noor E, Bar-Even A, Milo R (2012) eQuilibrator – the biochemical thermodynamics calculator. Nucleic Acids Res 40:D770–D775. https://doi.org/10.1093/nar/gkr874

    Article  CAS  PubMed  Google Scholar 

  41. Beber ME, Gollub MG, Mozaffari D, Shebek KM, Flamholz AI, Milo R et al (2022) eQuilibrator 3.0: a database solution for thermodynamic constant estimation. Nucleic Acids Res 50(D1):D603–D6D9. https://doi.org/10.1093/nar/gkab1106

    Article  CAS  PubMed  Google Scholar 

  42. Meng D, Liang A, Wei X, You C (2019) Enzymatic characterization of a thermostable phosphatase from Thermomicrobium roseum and its application for biosynthesis of fructose from maltodextrin. Appl Microbiol Biotechnol 103(15):6129–6139. https://doi.org/10.1007/s00253-019-09917-6

    Article  CAS  PubMed  Google Scholar 

  43. Dai Y, Zhang J, Zhang T, Chen J, Hassanin HA, Jiang B (2020) Characteristics of a fructose 6-phosphate 4-epimerase from Caldilinea aerophila DSM 14535 and its application for biosynthesis of tagatose. Enzym Microb Technol 139:109594. https://doi.org/10.1016/j.enzmictec.2020.109594

    Article  CAS  Google Scholar 

  44. Hu C, Wei X, Song Y (2022) A thermophilic phosphatase from Methanothermobacter marburgensis and its application to in vitro biosynthesis. Enzym Microb Technol 159:110067. https://doi.org/10.1016/j.enzmictec.2022.110067

    Article  CAS  Google Scholar 

  45. Tian C, Yang J, Li Y, Zhang T, Li J, Ren C et al (2020) Artificially designed routes for the conversion of starch to value-added mannosyl compounds through coupling in vitro and in vivo metabolic engineering strategies. Metab Eng 61:215–224. https://doi.org/10.1016/j.ymben.2020.06.008

    Article  CAS  PubMed  Google Scholar 

  46. Guterl JK, Garbe D, Carsten J, Steffler F, Sommer B, Reisse S et al (2012) Cell-free metabolic engineering: production of chemicals by minimized reaction cascades. ChemSusChem 5(11):2165–2172. https://doi.org/10.1002/cssc.201200365

    Article  CAS  PubMed  Google Scholar 

  47. Opgenorth PH, Korman TP, Iancu L, Bowie JU (2017) A molecular rheostat maintains ATP levels to drive a synthetic biochemistry system. Nat Chem Biol 13(9):938–942. https://doi.org/10.1038/nchembio.2418

    Article  CAS  PubMed  Google Scholar 

  48. Bai X, Meng D, Wei X, Zhou X, Lu F, You C (2019) Facile synthesis of (−)-vibo-quercitol from maltodextrin via an in vitro synthetic enzymatic biosystem. Biotechnol Bioeng 116(10):2710–2719. https://doi.org/10.1002/bit.27096

    Article  CAS  PubMed  Google Scholar 

  49. Satoh Y, Tajima K, Tannai H, Munekata M (2003) Enzyme-catalyzed poly(3-hydroxybutyrate) synthesis from acetate with CoA recycling and NADPH regeneration in vitro. J Biosci Bioeng 95(4):335–341

    Article  CAS  PubMed  Google Scholar 

  50. Xu ZN, Jing KJ, Liu Y, Cen PL (2007) High-level expression of recombinant glucose dehydrogenase and its application in NADPH regeneration. J Ind Microbiol Biotechnol 34(1):83–90. https://doi.org/10.1007/s10295-006-0168-2

    Article  CAS  PubMed  Google Scholar 

  51. Relyea HA, van der Donk WA (2005) Mechanism and applications of phosphite dehydrogenase. Bioorg Chem 33(3):171–189. https://doi.org/10.1016/j.bioorg.2005.01.003

    Article  CAS  PubMed  Google Scholar 

  52. Song YH, Liu MX, Xie LP, You C, Sun JS, Zhang Y-HPJ (2019) A recombinant 12-His tagged Pyrococcus furiosus soluble [NiFe]-hydrogenase I overexpressed in Thermococcus kodakarensis KOD1 facilitates hydrogen-powered in vitro NADH regeneration. Biotechnol J 14(4):e1800301. https://doi.org/10.1002/biot.201800301

    Article  CAS  PubMed  Google Scholar 

  53. Chen H, Zhang Y-HPJ (2021) Enzymatic regeneration and conservation of ATP: challenges and opportunities. Crit Rev Biotechnol 41(1):16–33. https://doi.org/10.1080/07388551.2020.1826403

    Article  CAS  PubMed  Google Scholar 

  54. Zhang X, Wu H, Huang B, Li ZM, Ye Q (2017) One-pot synthesis of glutathione by a two-enzyme cascade using a thermophilic ATP regeneration system. J Biotechnol 241:163–169. https://doi.org/10.1016/j.jbiotec.2016.11.034

    Article  CAS  PubMed  Google Scholar 

  55. Kamp AV, Klamt S (2020) MEMO: a method for computing metabolic modules for cell-free production systems. ACS Synth Biol 9(3):556–566. https://doi.org/10.1021/acssynbio.9b00434

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Kim DM, Swartz JR (2001) Regeneration of adenosine triphosphate from glycolytic intermediates for cell-free protein synthesis. Biotechnol Bioeng 74:309–316. https://doi.org/10.1002/bit.1121

    Article  CAS  PubMed  Google Scholar 

  57. Wang Y, Zhang Y-HP (2009) Cell-free protein synthesis energized by slowly-metabolized maltodextrin. BMC Biotechnol 9(1):58. https://doi.org/10.1186/1472-6750-9-58

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Wei X, Xie L, Zhang Y-HPJ, You C (2018) Stoichiometric regeneration of ATP by a NAD(P)/CoA-free and phosphate-balanced in vitro synthetic enzymatic biosystem. ChemCatChem 10(24):5597–5601. https://doi.org/10.1002/cctc.201801562

    Article  CAS  Google Scholar 

  59. Song H, Ma C, Liu P, You C, Lin J, Zhu Z (2019) A hybrid CO2 electroreduction system mediated by enzyme-cofactor conjugates coupled with Cu nanoparticle-catalyzed cofactor regeneration. J CO2 Util 34:568–575. https://doi.org/10.1016/j.jcou.2019.08.007

    Article  CAS  Google Scholar 

  60. Zhang S, Shi J, Sun Y, Wu Y, Zhang Y, Cai Z et al (2019) Artificial thylakoid for the coordinated photoenzymatic reduction of carbon dioxide. ACS Catal 9(5):3913–3925. https://doi.org/10.1021/acscatal.9b00255

    Article  CAS  Google Scholar 

  61. Fessner W-D, Walter C (1992) “Artificial metabolisms” for the asymmetric one-pot synthesis of branched-chain saccharides. Angew Chem Int Ed 31(5):614–616. https://doi.org/10.1002/anie.199206141

    Article  Google Scholar 

  62. Zimmermann FT, Schneider A, Schörken U, Sprenger GA, Fessner W-D (1999) Efficient multi-enzymatic synthesis of D-xylulose 5-phosphate. Tetrahedron Asymmetry 10(9):1643–1646. https://doi.org/10.1016/S0957-4166(99)00166-4

    Article  CAS  Google Scholar 

  63. Wang L, Dash S, Ng CY, Maranas CD (2017) A review of computational tools for design and reconstruction of metabolic pathways. Synth Syst Biotechnol 2(4):243–252. https://doi.org/10.1016/j.synbio.2017.11.002

    Article  PubMed  PubMed Central  Google Scholar 

  64. Li QK, Wang Z, Zhang M, Hou PF, Kang P (2017) Nitrogen doped tin oxide nanostructured catalysts for selective electrochemical reduction of carbon dioxide to formate. J Energy Chem 26(5):825–829. https://doi.org/10.1016/j.jechem.2017.08.010

    Article  Google Scholar 

  65. Wang J, Li G, Li Z, Tang C, Feng Z, An H et al (2017) A highly selective and stable ZnO-ZrO2 solid solution catalyst for CO2 hydrogenation to methanol. Sci Adv 3(10):e1701290. https://doi.org/10.1126/sciadv.1701290

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Ebrahim A, Lerman JA, Palsson BO, Hyduke DR (2013) COBRApy: COnstraints-based reconstruction and analysis for python. BMC Syst Biol 7:74. https://doi.org/10.1186/1752-0509-7-74

    Article  PubMed  PubMed Central  Google Scholar 

  67. Yang X, Yuan Q, Luo H, Li F, Mao Y, Zhao X et al (2019) Systematic design and in vitro validation of novel one-carbon assimilation pathways. Metab Eng 56:142–153. https://doi.org/10.1016/j.ymben.2019.09.001

    Article  CAS  PubMed  Google Scholar 

  68. Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM et al (2016) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 44(D1):D471–D480. https://doi.org/10.1093/nar/gkv1164

    Article  CAS  PubMed  Google Scholar 

  69. Hadadi N, Hafner J, Shajkofci A, Zisaki A, Hatzimanikatis V (2016) ATLAS of biochemistry: a repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies. ACS Synth Biol 5(10):1155–1166. https://doi.org/10.1021/acssynbio.6b00054

    Article  CAS  PubMed  Google Scholar 

  70. Jang WD, Kim GB, Kim Y, Lee SY (2022) Applications of artificial intelligence to enzyme and pathway design for metabolic engineering. Curr Opin Biotechnol 73:101–107. https://doi.org/10.1016/j.copbio.2021.07.024

    Article  CAS  PubMed  Google Scholar 

  71. Koch M, Duigou T, Faulon J-L (2020) Reinforcement learning for bioretrosynthesis. ACS Synth Biol 9(1):157–168. https://doi.org/10.1021/acssynbio.9b00447

    Article  CAS  PubMed  Google Scholar 

  72. Wei X, Meng D, You C (2020) In vitro metabolic engineering: current status and recent progress. In: Liu L, Du GC, Liu YF (eds) Systems and synthetic metabolic engineering. Elsevier, pp 183–206

    Chapter  Google Scholar 

  73. Maini Rekdal V, Bess EN, Bisanz JE, Turnbaugh PJ, Balskus EP (2019) Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism. Science 364(6445). https://doi.org/10.1126/science.aau6323

  74. Li G, Ren J, Wu Q, Feng J, Zhu D, Ma Y (2013) Identification of a marine NADPH-dependent aldehyde reductase for chemoselective reduction of aldehydes. J Mol Catal B Enzym 90:17–22. https://doi.org/10.1016/j.molcatb.2013.01.010

    Article  CAS  Google Scholar 

  75. Jia B, Han X, Kim KH, Jeon CO (2022) Discovery and mining of enzymes from the human gut microbiome. Trends Biotechnol 40(2):240–254. https://doi.org/10.1016/j.tibtech.2021.06.008

    Article  CAS  PubMed  Google Scholar 

  76. Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L et al (2012) Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc Natl Acad Sci U S A 109(11):4122–4127. https://doi.org/10.1073/pnas.1112081109

    Article  PubMed  PubMed Central  Google Scholar 

  77. Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR et al (2015) Enzyme function initiative-enzyme similarity tool (EFI-EST): a web tool for generating protein sequence similarity networks. Biochim Biophys Acta 1854(8):1019–1037. https://doi.org/10.1016/j.bbapap.2015.04.015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Burroughs AM, Allen KN, Dunaway-Mariano D, Aravind L (2006) Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. J Mol Biol 361(5):1003–1034. https://doi.org/10.1016/j.jmb.2006.06.049

    Article  CAS  PubMed  Google Scholar 

  79. Ren H, Shi C, Zhao H (2020) Computational tools for discovering and engineering natural product biosynthetic pathways. iScience 23(1):100795. https://doi.org/10.1016/j.isci.2019.100795

    Article  PubMed  Google Scholar 

  80. Yang G, Hong S, Yang P, Sun Y, Wang Y, Zhang P et al (2021) Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria. Nat Commun 12(1):790. https://doi.org/10.1038/s41467-021-20974-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Ely B (2020) Recombination and gene loss occur simultaneously during bacterial horizontal gene transfer. PLoS One 15(1):e0227987. https://doi.org/10.1371/journal.pone.0227987

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D et al (2015) Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nat Commun 6:10005. https://doi.org/10.1038/ncomms10005

    Article  CAS  PubMed  Google Scholar 

  83. Song Y, DiMaio F, Wang RY, Kim D, Miles C, Brunette T et al (2013) High-resolution comparative modeling with RosettaCM. Structure 21(10):1735–1742. https://doi.org/10.1016/j.str.2013.08.005

    Article  CAS  PubMed  Google Scholar 

  84. Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33(7):2302–2309. https://doi.org/10.1093/nar/gki524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Bonetta R, Valentino G (2020) Machine learning techniques for protein function prediction. Proteins: Struct, Funct, Bioinf 88(3):397–413. https://doi.org/10.1002/prot.25832

    Article  CAS  Google Scholar 

  86. Dalkiran A, Rifaioglu AS, Martin MJ, Cetin-Atalay R, Atalay V, Doğan T (2018) ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature. BMC Bioinformatics 19(1):334. https://doi.org/10.1186/s12859-018-2368-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. De Ferrari L, Mitchell JB (2014) From sequence to enzyme mechanism using multi-label machine learning. BMC Bioinformatics 15:150. https://doi.org/10.1186/1471-2105-15-150

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Reetz MT, Sun Z, Ge Q (2023) Enzyme engineering: selective catalysts for applications in biotechnology, organic chemistry, and life science. Wiley, Weinheim

    Book  Google Scholar 

  89. Singh RK, Tiwari MK, Singh R, Lee JK (2013) From protein engineering to immobilization: promising strategies for the upgrade of industrial enzymes. Int J Mol Sci 14(1):1232–1277. https://doi.org/10.3390/ijms14011232

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Cedrone F, Menez A, Quemeneur E (2000) Tailoring new enzyme functions by rational redesign. Curr Opin Struct Biol 10(4):405–410. https://doi.org/10.1016/s0959-440x(00)00106-8

    Article  CAS  PubMed  Google Scholar 

  91. Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R et al (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46(W1):W296–w303. https://doi.org/10.1093/nar/gky427

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y (2015) The I-TASSER suite: protein structure and function prediction. Nat Methods 12(1):7–8. https://doi.org/10.1038/nmeth.3213

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Senior AW, Evans R, Jumper J, Kirkpatrick J, Sifre L, Green T et al (2020) Improved protein structure prediction using potentials from deep learning. Nature 577(7792):706–710. https://doi.org/10.1038/s41586-019-1923-7

    Article  CAS  PubMed  Google Scholar 

  94. Taylor RD, Jewsbury PJ, Essex JW (2002) A review of protein-small molecule docking methods. J Comput Aided Mol Des 16(3):151–166. https://doi.org/10.1023/a:1020155510718

    Article  CAS  PubMed  Google Scholar 

  95. Yang C, Chen EA, Zhang Y (2022) Protein-ligand docking in the machine-learning era. Molecules 27(14). https://doi.org/10.3390/molecules27144568

  96. Tobe S, Shimogaki H, Ohdera M, Asai Y, Oba K, Iwama M et al (2006) Expression of Bacillus protease (Protease BYA) from Bacillus sp. Y in Bacillus subtilis and enhancement of its specific activity by site-directed mutagenesis-improvement in productivity of detergent enzyme. Biol Pharm Bull 29(1):26–33. https://doi.org/10.1248/bpb.29.26

    Article  CAS  PubMed  Google Scholar 

  97. Lee S, Lee DG, Jang MK, Jeon MJ, Jang HJ, Lee SH (2011) Improvement in the catalytic activity of β-agarase AgaA from Zobellia galactanivorans by site-directed mutagenesis. J Microbiol Biotechnol 21(11):1116–1122. https://doi.org/10.4014/jmb.1107.07001

    Article  CAS  PubMed  Google Scholar 

  98. Renugopalakrishnan V, Garduno-Juarez R, Narasimhan G, Verma CS, Wei X, Li P (2005) Rational design of thermally stable proteins: relevance to bionanotechnology. J Nanosci Nanotechnol 5(11):1759–1767. https://doi.org/10.1166/jnn.2005.441

    Article  CAS  PubMed  Google Scholar 

  99. Yu H, Yan Y, Zhang C, Dalby PA (2017) Two strategies to engineer flexible loops for improved enzyme thermostability. Sci Rep 7:41212. https://doi.org/10.1038/srep41212

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Chuaboon L, Wongnate T, Punthong P, Kiattisewee C, Lawan N, Hsu CY et al (2019) One-pot bioconversion of L-arabinose to L-ribulose in an enzymatic cascade. Angew Chem Int Ed 58(8):2428–2432. https://doi.org/10.1002/anie.201814219

    Article  CAS  Google Scholar 

  101. Roda S, Fernandez-Lopez L, Cañadas R, Santiago G, Ferrer M, Guallar V (2021) Computationally driven rational design of substrate promiscuity on serine ester hydrolases. ACS Catal 11(6):3590–3601. https://doi.org/10.1021/acscatal.0c05015

    Article  CAS  Google Scholar 

  102. Chen H, Zhu ZG, Huang R, Zhang Y-HP (2016) Coenzyme engineering of a hyperthermophilic 6-phosphogluconate dehydrogenase from NADP+ to NAD+ with its application to biobatteries. Sci Rep 6:36311. https://doi.org/10.1038/srep36311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Xu LH, Du YL (2018) Rational and semi-rational engineering of cytochrome P450s for biotechnological applications. Synth Syst Biotechnol 3(4):283–290. https://doi.org/10.1016/j.synbio.2018.10.001

    Article  PubMed  PubMed Central  Google Scholar 

  104. Chica RA, Doucet N, Pelletier JN (2005) Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. Curr Opin Biotechnol 16(4):378–384. https://doi.org/10.1016/j.copbio.2005.06.004

    Article  CAS  PubMed  Google Scholar 

  105. Voigt CA, Kauffman S, Wang ZG (2000) Rational evolutionary design: the theory of in vitro protein evolution. Adv Protein Chem 55:79–160. https://doi.org/10.1016/s0065-3233(01)55003-2

    Article  CAS  PubMed  Google Scholar 

  106. Reetz MT, Carballeira JD (2007) Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat Protoc 2(4):891–903. https://doi.org/10.1038/nprot.2007.72

    Article  CAS  PubMed  Google Scholar 

  107. Reetz MT, Wu S (2008) Greatly reduced amino acid alphabets in directed evolution: making the right choice for saturation mutagenesis at homologous enzyme positions. Chem Commun (Camb) 43:5499–5501. https://doi.org/10.1039/b813388c

    Article  CAS  Google Scholar 

  108. Dwyer MA, Looger LL, Hellinga HW (2004) Computational design of a biologically active enzyme. Science 304(5679):1967–1971. https://doi.org/10.1126/science.1098432

    Article  CAS  PubMed  Google Scholar 

  109. Reetz MT (2016) Selected examples of directed evolution of enzymes with emphasis on stereo- and regioselectivity, substrate scope, and/or activity. Directed evolution of selective enzymes: catalysts for organic chemistry and biotechnology, pp 167–203

    Google Scholar 

  110. Huang R, Chen H, Zhong C, Kim JE, Zhang YH (2016) High-throughput screening of coenzyme preference change of thermophilic 6-phosphogluconate dehydrogenase from NADP+ to NAD+. Sci Rep 6:32644. https://doi.org/10.1038/srep32644

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Huang R, Chen H, Zhou W, Ma C, Zhang YP (2018) Engineering a thermostable highly active glucose 6-phosphate dehydrogenase and its application to hydrogen production in vitro. Appl Microbiol Biotechnol 102(7):3203–3215. https://doi.org/10.1007/s00253-018-8798-7

    Article  CAS  PubMed  Google Scholar 

  112. Ma C, Liu M, You C, Zhu Z (2020) Engineering a diaphorase via directed evolution for enzymatic biofuel cell application. Bioresour Bioprocess 7(1):23. https://doi.org/10.1186/s40643-020-00311-z

    Article  Google Scholar 

  113. Zhou W, Huang R, Zhu ZG, Zhang Y-HPJ (2018) Coevolution of both thermostability and activity of polyphosphate glucokinase from Thermobifida fusca YX. Appl Environ Microbiol 84(16):e01224–e01218. https://doi.org/10.1128/AEM.01224-18

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Yang KK, Wu Z, Arnold FH (2019) Machine-learning-guided directed evolution for protein engineering. Nat Methods 16(8):687–694. https://doi.org/10.1038/s41592-019-0496-6

    Article  CAS  PubMed  Google Scholar 

  115. Wittmann BJ, Johnston KE, Wu Z, Arnold FH (2021) Advances in machine learning for directed evolution. Curr Opin Struct Biol 69:11–18. https://doi.org/10.1016/j.sbi.2021.01.008

    Article  CAS  PubMed  Google Scholar 

  116. Fox RJ, Davis SC, Mundorff EC, Newman LM, Gavrilovic V, Ma SK et al (2007) Improving catalytic function by ProSAR-driven enzyme evolution. Nat Biotechnol 25(3):338–344. https://doi.org/10.1038/nbt1286

    Article  CAS  PubMed  Google Scholar 

  117. You C, Myung S, Zhang Y-HP (2012) Facilitated substrate channeling in a self-assembled trifunctional enzyme complex. Angew Chem Int Ed 51(35):8787–8790. https://doi.org/10.1002/anie.201202441

    Article  CAS  Google Scholar 

  118. Han P, You C, Li Y, Shi T, Wu H, Zhang Y-HPJ (2023) High-titer production of myo-inositol by a co-immobilized four-enzyme cocktail in biomimetic mineralized microcapsules. Chem Eng J 461:141946. https://doi.org/10.1016/j.cej.2023.141946

    Article  CAS  Google Scholar 

  119. Bauler P, Huber G, Leyh T, McCammon JA (2010) Channeling by proximity: the catalytic advantages of active site colocalization using Brownian dynamics. J Phys Chem Lett 1(9):1332–1335. https://doi.org/10.1021/jz1002007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Fan LW, Wang Y, Tuyishime P, Gao N, Li QG, Zheng P et al (2018) Engineering artificial fusion proteins for enhanced methanol bioconversion. ChemBioChem 19(23):2465–2471. https://doi.org/10.1002/cbic.201800424

    Article  CAS  PubMed  Google Scholar 

  121. Zakeri B, Fierer JO, Celik E, Chittock EC, Schwarz-Linek U, Moy VT et al (2012) Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Proc Natl Acad Sci U S A 109(12):E690–E697. https://doi.org/10.1073/pnas.1115485109

    Article  PubMed  PubMed Central  Google Scholar 

  122. Fierobe HP, Mechaly A, Tardif C, Belaich A, Lamed R, Shoham Y et al (2001) Design and production of active cellulosome chimeras. Selective incorporation of dockerin-containing enzymes into defined functional complexes. J Biol Chem 276(24):21257–21261. https://doi.org/10.1074/jbc.M102082200

    Article  CAS  PubMed  Google Scholar 

  123. Fierobe HP, Bayer EA, Tardif C, Czjzek M, Mechaly A, Belaich A et al (2002) Degradation of cellulose substrates by cellulosome chimeras. Substrate targeting versus proximity of enzyme components. J Biol Chem 277(51):49621–49630. https://doi.org/10.1074/jbc.M207672200

    Article  CAS  PubMed  Google Scholar 

  124. Liu M, Song Y, Zhang YPJ, You C (2022) Carrier-free immobilization of multi-enzyme complex facilitates in vitro synthetic enzymatic biosystem for biomanufacturing. ChemSusChem:e202202153. https://doi.org/10.1002/cssc.202202153

  125. Meng D, Wu R, Wang J, Zhu Z, You C (2019) Acceleration of cellodextrin phosphorolysis for bioelectricity generation from cellulosic biomass by integrating a synthetic two-enzyme complex into an in vitro synthetic enzymatic biosystem. Biotechnol Biofuels 12:267. https://doi.org/10.1186/s13068-019-1607-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Chen H, Huang R, Kim E-J, Zhang Y-HPJ (2018) Building a thermostable metabolon for facilitating coenzyme transport and in vitro hydrogen production at elevated temperature. ChemSusChem 11(18):3120–3130. https://doi.org/10.1002/cssc.201801141

    Article  CAS  PubMed  Google Scholar 

  127. Sheldon RA, van Pelt S (2013) Enzyme immobilisation in biocatalysis: why, what and how. Chem Soc Rev 42(15):6223–6235. https://doi.org/10.1039/c3cs60075k

    Article  CAS  PubMed  Google Scholar 

  128. Han P, Zhou X, You C (2020) Efficient multi-enzymes immobilized on porous microspheres for producing inositol from starch. Front Bioeng Biotechnol:8. https://doi.org/10.3389/fbioe.2020.00380

  129. Talekar S, Joshi A, Kambale S, Jadhav S, Nadar S, Ladole M (2017) A tri-enzyme magnetic nanobiocatalyst with one pot starch hydrolytic activity. Chem Eng J 325:80–90. https://doi.org/10.1016/j.cej.2017.05.054

    Article  CAS  Google Scholar 

  130. Su HH, Guo ZW, Wu XL, Xu P, Li N, Zong MH et al (2019) Efficient bioconversion of sucrose to high-value-added glucaric acid by in vitro metabolic engineering. ChemSusChem 12(10):2278–2285. https://doi.org/10.1002/cssc.201900185

    Article  CAS  PubMed  Google Scholar 

  131. Li G, Wei X, Wu R, Zhou W, Li Y, Zhu Z et al (2022) Stoichiometric conversion of maltose for biomanufacturing by in vitro synthetic enzymatic biosystems. BioDesign Res 2022. https://doi.org/10.34133/2022/9806749

  132. Zhong C, Wei P, Zhang Y-HP (2017) A kinetic model of one-pot rapid biotransformation of cellobiose from sucrose catalyzed by three thermophilic enzymes. Chem Eng Sci 161:159–166. https://doi.org/10.1016/j.ces.2016.11.047

    Article  CAS  Google Scholar 

  133. Korman TP, Opgenorth PH, Bowie JU (2017) A synthetic biochemistry platform for cell free production of monoterpenes from glucose. Nat Commun 8:15526. https://doi.org/10.1038/ncomms15526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Takors R (2012) Scale-up of microbial processes: impacts, tools and open questions. J Biotechnol 160(1–2):3–9. https://doi.org/10.1016/j.jbiotec.2011.12.010

    Article  CAS  PubMed  Google Scholar 

  135. Dudley QM, Karim AS, Jewett MC (2015) Cell-free metabolic engineering: biomanufacturing beyond the cell. Biotechnol J 10(1):69–82. https://doi.org/10.1002/biot.201400330

    Article  CAS  PubMed  Google Scholar 

  136. Han P, Wang X, Li Y, Wu H, Shi T, Shi J (2023) Synthesis of a healthy sweetener D-tagatose from starch catalyzed by semiartificial cell factories. J Agric Food Chem 71(8):3813–3820. https://doi.org/10.1021/acs.jafc.2c08400

    Article  CAS  PubMed  Google Scholar 

  137. Xu X, Zhang W, You C, Fan C, Ji W, Park J-T et al (2023) Biosynthesis of artificial starch and microbial protein from agricultural residue. Sci Bull 68(2):214–223. https://doi.org/10.1016/j.scib.2023.01.006

    Article  CAS  Google Scholar 

  138. Ye J, Li Y, Bai Y, Zhang T, Jiang W, Shi T et al (2022) A facile and robust T7-promoter-based high-expression of heterologous proteins in Bacillus subtilis. Bioresour Bioprocess 9(1):56. https://doi.org/10.1186/s40643-022-00540-4

    Article  Google Scholar 

  139. Kim JE, Kim EJ, Chen H, Wu CH, Adams MWW, Zhang Y-HP (2017) Advanced water splitting for green hydrogen gas production through complete oxidation of starch by in vitro metabolic engineering. Metab Eng 44:246–252. https://doi.org/10.1016/j.ymben.2017.09.015

    Article  CAS  PubMed  Google Scholar 

  140. Lovelock SL, Crawshaw R, Basler S, Levy C, Baker D, Hilvert D et al (2022) The road to fully programmable protein catalysis. Nature 606(7912):49–58. https://doi.org/10.1038/s41586-022-04456-z

    Article  CAS  PubMed  Google Scholar 

  141. Yeh AH-W, Norn C, Kipnis Y, Tischer D, Pellock SJ, Evans D et al (2023) De novo design of luciferases using deep learning. Nature 614(7949):774–780. https://doi.org/10.1038/s41586-023-05696-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Nikolados EM, Wongprommoon A, Aodha OM, Cambray G, Oyarzun DA (2022) Accuracy and data efficiency in deep learning models of protein expression. Nat Commun 13(1):7755. https://doi.org/10.1038/s41467-022-34902-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

We are grateful to Professor Yi-Heng P. Job Zhang, the director of in vitro Synthetic Biology Center of TIB, CAS, for providing scientific suggestions.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Xinlei Wei or Chun You .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Qin, Y., Li, Q., Fan, L., Ning, X., Wei, X., You, C. (2023). Biomanufacturing by In Vitro Biotransformation (ivBT) Using Purified Cascade Multi-enzymes. In: Lu, Y., Jewett, M.C. (eds) Cell-free Production. Advances in Biochemical Engineering/Biotechnology, vol 186. Springer, Cham. https://doi.org/10.1007/10_2023_231

Download citation

Publish with us

Policies and ethics