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Strategies for Multienzyme Assemblies

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Multienzymatic Assemblies

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2487))

Abstract

Proteins are not designed to be standalone entities and must coordinate their collective action for optimum performance. Nature has developed through evolution the ability to co-localize the functional partners of a cascade enzymatic reaction in order to ensure efficient exchange of intermediates. Inspired by these natural designs, synthetic scaffolds have been created to enhance the overall biological pathway performance. In this chapter, we describe several DNA- and protein-based scaffold approaches to assemble artificial enzyme cascades for a wide range of applications. We highlight the key benefits and drawbacks of these approaches to provide insights on how to choose the appropriate scaffold for different cascade systems.

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References

  1. Chen Q, Rozovsky S, Chen W (2017) Engineering multi-functional bacterial outer membrane vesicles as modular nanodevices for biosensing and bioimaging. Chem Commun 53(54):7569–7572

    Article  CAS  Google Scholar 

  2. Chen Q, Sun Q, Molino NM, Wang S-W, Boder ET, Chen W (2015) Sortase A-mediated multi-functionalization of protein nanoparticles. Chem Commun 51(60):12107–12110

    Article  CAS  Google Scholar 

  3. Liu F, Banta S, Chen W (2013) Functional assembly of a multi-enzyme methanol oxidation cascade on a surface-displayed trifunctional scaffold for enhanced NADH production. Chem Commun 49(36):3766–3768

    Article  CAS  Google Scholar 

  4. Tsai SL, DaSilva NA, Chen W (2013) Functional display of complex cellulosomes on the yeast surface via adaptive assembly. ACS Synth Biol 2(1):14–21

    Article  CAS  PubMed  Google Scholar 

  5. Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, Keasling JD (2009) Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol 27(8):753–759

    Article  CAS  PubMed  Google Scholar 

  6. Berckman EA, Chen W (2019) Exploiting dCas9 fusion proteins for dynamic assembly of synthetic metabolons. Chem Commun 55(57):8219–8222

    Article  CAS  Google Scholar 

  7. Zhao EM, Suek N, Wilson MZ, Dine E, Pannucci NL, Gitai Z, Avalos JL, Toettcher JE (2019) Light-based control of metabolic flux through assembly of synthetic organelles. Nat Chem Biol 15(6):589–597

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Park M, Sun Q, Liu F, DeLisa MP, Chen W (2014) Positional assembly of enzymes on bacterial outer membrane vesicles for cascade reactions. PLoS One 9(5):6

    Google Scholar 

  9. Wheeldon I, Minteer SD, Banta S, Barton SC, Atanassov P, Sigman M (2016) Substrate channelling as an approach to cascade reactions. Nat Chem 8(4):299–309

    Article  CAS  PubMed  Google Scholar 

  10. Sun Q, Tsai S-L, Chen W (2019) Artificial scaffolds for enhanced biocatalysis. In: Schmidt-Dannert C, Quin MB (eds) Methods in enzymology, vol 617. Academic Press, Cambridge, pp 363–383

    Google Scholar 

  11. Price JV, Chen L, Whitaker WB, Papoutsakis E, Chen W (2016) Scaffoldless engineered enzyme assembly for enhanced methanol utilization. Proc Natl Acad Sci 113(45):12691–12696

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Sun Q, Chen W (2016) HaloTag mediated artificial cellulosome assembly on a rolling circle amplification DNA template for efficient cellulose hydrolysis. Chem Commun 52(40):6701–6704

    Article  CAS  Google Scholar 

  13. Chen Q, Yu S, Myung N, Chen W (2017) DNA-guided assembly of a five-component enzyme cascade for enhanced conversion of cellulose to gluconic acid and H2O2. J Biotechnol 263:30–35

    Article  CAS  PubMed  Google Scholar 

  14. Lee H, DeLoache WC, Dueber JE (2012) Spatial organization of enzymes for metabolic engineering. Metab Eng 14(3):242–251

    Article  CAS  PubMed  Google Scholar 

  15. Gao X, Yang S, Zhao C, Ren Y, Wei D (2014) Artificial multienzyme supramolecular device: highly ordered self-assembly of oligomeric enzymes in vitro and in vivo. Angew Chem Int Ed Engl 53(51):14027–14030

    Article  CAS  PubMed  Google Scholar 

  16. Qu J, Cao S, Wei Q, Zhang H, Wang R, Kang W, Ma T, Zhang L, Liu T, Wing-Ngor Au S, Sun F, Xia J (2019) Synthetic multienzyme complexes, catalytic nanomachineries for cascade biosynthesis in vivo. ACS Nano 13(9):9895–9906

    Article  CAS  PubMed  Google Scholar 

  17. Garbett D, Bretscher A (2014) The surprising dynamics of scaffolding proteins. Mol Biol Cell 25(16):2315–2319

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Sun Q, Madan B, Tsai SL, DeLisa MP, Chen W (2014) Creation of artificial cellulosomes on DNA scaffolds by zinc finger protein-guided assembly for efficient cellulose hydrolysis. Chem Commun 50(12):1423–1425

    Article  CAS  Google Scholar 

  19. Tsai SL, Oh J, Singh S, Chen RZ, Chen W (2009) Functional assembly of minicellulosomes on the saccharomyces cerevisiae cell surface for cellulose hydrolysis and ethanol production. Appl Environ Microbiol 75(19):6087–6093

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Tsai SL, Goyal G, Chen W (2010) Surface display of a functional minicellulosome by intracellular complementation using a synthetic yeast consortium and its application to cellulose hydrolysis and ethanol production. Appl Environ Microbiol 76(22):7514–7520

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Goyal G, Tsai SL, Madan B, DaSilva NA, Chen W (2011) Simultaneous cell growth and ethanol production from cellulose by an engineered yeast consortium displaying a functional mini-cellulosome. Microb Cell Factories 10:8

    Article  CAS  Google Scholar 

  22. Gilbert HJ (2007) Cellulosomes: microbial nanomachines that display plasticity in quaternary structure. Mol Microbiol 63(6):1568–1576

    Article  CAS  PubMed  Google Scholar 

  23. Bayer EA, Belaich JP, Shoham Y, Lamed R (2004) The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu Rev Microbiol 58:521–554

    Article  CAS  PubMed  Google Scholar 

  24. Fierobe H-P, Mingardon F, Mechaly A, Bélaïch A, Rincon MT, Pagès S, Lamed R, Tardif C, Bélaïch J-P, Bayer EA (2005) Action of designer cellulosomes on homogeneous versus complex substrates: controlled incorporation of three distinct enzymes into a defined trifunctional scaffoldin. J Biol Chem 280(16):16325–16334

    Article  CAS  PubMed  Google Scholar 

  25. You C, Myung S, Zhang YHP (2012) Facilitated substrate channeling in a self-assembled trifunctional enzyme complex. Angew Chem Int Ed 51(35):8787–8790

    Article  CAS  Google Scholar 

  26. You C, Zhang YHP (2013) Self-assembly of synthetic metabolons through synthetic protein scaffolds: one-step purification, co-immobilization, and substrate channeling. ACS Synth Biol 2(2):102–110

    Article  CAS  PubMed  Google Scholar 

  27. Lee EJ, Lee NK, Kim I-S (2016) Bioengineered protein-based nanocage for drug delivery. Adv Drug Deliv Rev 106:157–171

    Article  CAS  PubMed  Google Scholar 

  28. Zdanowicz M, Chroboczek J (2016) Virus-like particles as drug delivery vectors. Acta Biochim Pol 63(3):469–473

    Article  CAS  PubMed  Google Scholar 

  29. Hartzell EJ, Lieser RM, Sullivan MO, Chen W (2020) Modular hepatitis B virus-like particle platform for biosensing and drug delivery. ACS Nano 14(10):12642–12651

    Article  CAS  PubMed  Google Scholar 

  30. MacKay JA, Chen M, McDaniel JR, Liu W, Simnick AJ, Chilkoti A (2009) Self-assembling chimeric polypeptide-doxorubicin conjugate nanoparticles that abolish tumours after a single injection. Nat Mater 8(12):993–999

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  31. Estrada LH, Chu S, Champion JA (2014) Protein nanoparticles for intracellular delivery of therapeutic enzymes. J Pharm Sci 103(6):1863–1871

    Article  CAS  PubMed  Google Scholar 

  32. Lieser RM, Yur D, Sullivan MO, Chen W (2020) Site-specific bioconjugation approaches for enhanced delivery of protein therapeutics and protein drug carriers. Bioconjug Chem 31(10):2272–2282

    Article  CAS  PubMed  Google Scholar 

  33. Axup JY, Bajjuri KM, Ritland M, Hutchins BM, Kim CH, Kazane SA, Halder R, Forsyth JS, Santidrian AF, Stafin K, Lu Y, Tran H, Seller AJ, Biroc SL, Szydlik A, Pinkstaff JK, Tian F, Sinha SC, Felding-Habermann B, Smider VV, Schultz PG (2012) Synthesis of site-specific antibody-drug conjugates using unnatural amino acids. Proc Natl Acad Sci 109(40):16101–16106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Lyu Z, Kang L, Buuh ZY, Jiang D, McGuth JC, Du J, Wissler HL, Cai W, Wang RE (2018) A switchable site-specific antibody conjugate. ACS Chem Biol 13(4):958–964

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Berckman EA, Hartzell EJ, Mitkas AA, Sun Q, Chen W (2020) Biological assembly of modular protein building blocks as sensing, delivery, and therapeutic agents. Annu Rev Chem Biomol Eng 11(1):35–62

    Article  CAS  PubMed  Google Scholar 

  36. Khoshnejad M, Greineder CF, Pulsipher KW, Villa CH, Altun B, Pan DC, Tsourkas A, Dmochowski IJ, Muzykantov VR (2018) Ferritin nanocages with biologically orthogonal conjugation for vascular targeting and imaging. Bioconjug Chem 29(4):1209–1218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. ElSohly AM, Netirojjanakul C, Aanei IL, Jager A, Bendall SC, Farkas ME, Nolan GP, Francis MB (2015) Synthetically modified viral capsids as versatile carriers for use in antibody-based cell targeting. Bioconjug Chem 26(8):1590–1596

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Raeeszadeh-Sarmazdeh M, Hartzell E, Price JV, Chen W (2016) Protein nanoparticles as multifunctional biocatalysts and health assessment sensors. Curr Opin Chem Eng 13:109–118

    Article  PubMed  PubMed Central  Google Scholar 

  39. Raeeszadeh-Sarmazdeh M, Parthasarathy R, Boder ET (2015) Site-specific immobilization of protein layers on gold surfaces via orthogonal sortases. Colloids Surf B: Biointerfaces 128:457–463

    Article  CAS  PubMed  Google Scholar 

  40. Raeeszadeh-Sarmazdeh M, Parthasarathy R, Boder ET (2017) Fine-tuning sortase-mediated immobilization of protein layers on surfaces using sequential deprotection and coupling. Biotechnol Prog 33(3):824–831

    Article  CAS  PubMed  Google Scholar 

  41. Zakeri B, Fierer JO, Celik E, Chittock EC, Schwarz-Linek U, Moy VT, Howarth M (2012) Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Proc Natl Acad Sci 109(12):E690–E697

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Keeble AH, Howarth M (2020) Power to the protein: enhancing and combining activities using the Spy toolbox. Chem Sci 11(28):7281–7291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Berckman EA, Chen W (2020) A modular approach for dCas9-mediated enzyme cascading via orthogonal bioconjugation. Chem Commun 56:11426–11428

    Article  CAS  Google Scholar 

  44. Swartz AR, Sun Q, Chen W (2017) Ligand-induced cross-linking of Z-elastin-like polypeptide-functionalized E2 protein nanoparticles for enhanced affinity precipitation of antibodies. Biomacromolecules 18(5):1654–1659

    Article  CAS  PubMed  Google Scholar 

  45. Liu F, Tsai SL, Madan B, Chen W (2012) Engineering a high-affinity scaffold for non-chromatographic protein purification via intein-mediated cleavage. Biotechnol Bioeng 109(11):2829–2835

    Article  CAS  PubMed  Google Scholar 

  46. Madan B, Chaudhary G, Cramer SM, Chen W (2013) ELP-z and ELP-zz capturing scaffolds for the purification of immunoglobulins by affinity precipitation. J Biotechnol 163(1):10–16

    Article  CAS  PubMed  Google Scholar 

  47. Kim H, Siu KH, Raeeszadeh-Sarmazdeh M, Sun Q, Chen Q, Chen W (2015) Bioengineering strategies to generate artificial protein complexes. Biotechnol Bioeng 112(8):1495–1505

    Article  CAS  PubMed  Google Scholar 

  48. Levary DA, Parthasarathy R, Boder ET, Ackerman ME (2011) Protein-protein fusion catalyzed by sortase A. PLoS One 6(4):e18342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Parthasarathy R, Subramanian S, Boder ET (2007) Sortase A as a novel molecular “stapler” for sequence-specific protein conjugation. Bioconjug Chem 18(2):469–476

    Article  CAS  PubMed  Google Scholar 

  50. Wei Q, He S, Qu J, Xia J (2020) Synthetic multienzyme complexes assembled on virus-like particles for cascade biosynthesis in cellulo. Bioconjug Chem 31(10):2413–2420

    Article  CAS  PubMed  Google Scholar 

  51. Pinheiro AV, Han D, Shih WM, Yan H (2011) Challenges and opportunities for structural DNA nanotechnology. Nat Nanotechnol 6(12):763–772

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Blackstock D, Chen W (2014) Halo-tag mediated self-labeling of fluorescent proteins to molecular beacons for nucleic acid detection. Chem Commun 50(89):13735–13738

    Article  CAS  Google Scholar 

  53. Blackstock D, Sun Q, Chen W (2014) Fluorescent protein-based molecular beacons by zinc finger protein-guided assembly. Biotechnol Bioeng. 112(2):236–241

    Article  PubMed  CAS  Google Scholar 

  54. Chen RP, Blackstock D, Sun Q, Chen W (2018) Dynamic protein assembly by programmable DNA strand displacement. Nat Chem 10(4):474–481

    Article  PubMed  CAS  Google Scholar 

  55. Siu KH, Chen W (2019) Riboregulated toehold-gated gRNA for programmable CRISPR-Cas9 function. Nat Chem Biol 15(3):217–220

    Article  CAS  PubMed  Google Scholar 

  56. Los GV, Encell LP, McDougall MG, Hartzell DD, Karassina N, Zimprich C, Wood MG, Learish R, Ohana RF, Urh M, Simpson D, Mendez J, Zimmerman K, Otto P, Vidugiris G, Zhu J, Darzins A, Klaubert DH, Bulleit RF, Wood KV (2008) HaloTag: A novel protein labeling technology for cell imaging and protein analysis. ACS Chem Biol 3(6):373–382

    Article  CAS  PubMed  Google Scholar 

  57. Conrado RJ, Wu GC, Boock JT, Xu H, Chen SY, Lebar T, Turnšek J, Tomšič N, Avbelj M, Gaber R, Koprivnjak T, Mori J, Glavnik V, Vovk I, Benčina M, Hodnik V, Anderluh G, Dueber JE, Jerala R, DeLisa MP (2012) DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res 40(4):1879–1889

    Article  CAS  PubMed  Google Scholar 

  58. Choo Y, Isalan M (2000) Advances in zinc finger engineering. Curr Opin Struct Biol 10(4):411–416

    Article  CAS  PubMed  Google Scholar 

  59. Dhanasekaran M, Negi S, Sugiura Y (2006) Designer zinc finger proteins: tools for creating artificial DNA-binding functional proteins. Acc Chem Res 39(1):45–52

    Article  CAS  PubMed  Google Scholar 

  60. Siu KH, Chen RP, Sun Q, Chen L, Tsai SL, Chen W (2015) Synthetic scaffolds for pathway enhancement. Curr Opin Biotechnol 36:98–106

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This review was supported by grants from NSF (CBE1803008, CBE1911950, MCB1817675, MCB2013991, and DMR1609621).

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Correspondence to Wilfred Chen .

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Sun, Q., Raeeszadeh-Sarmazdeh, M., Tsai, SL., Chen, W. (2022). Strategies for Multienzyme Assemblies. In: Stamatis, H. (eds) Multienzymatic Assemblies. Methods in Molecular Biology, vol 2487. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2269-8_7

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  • DOI: https://doi.org/10.1007/978-1-0716-2269-8_7

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