Repurposing Photosensitizer Proteins Through Genetic Code Expansion to Facilitate Photo-Biocatalysis

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Genetically Incorporated Non-Canonical Amino Acids

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2676))

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Abstract

Artificial photoenzymes with noncanonical photo-redox cofactors have paved the way for enzyme rational design and the creation of new-to-nature biocatalysts. Genetically encoded photo-redox cofactors endow photoenzymes with enhanced or novel activities that catalyze numerous transformations with high efficiency. Herein, we describe a protocol of repurposing photosensitizer proteins (PSP) through genetic code expansion to facilitate multiple photocatalytic conversions including photo-activated dehalogenation of aryl halides, CO2 to CO and CO2 to formic acid reduction. The methods for expression, purification, and characterization of the PSP are detailed. The installation of the catalytic modules and the utilization of PSP-based artificial photoenzymes for photoenzymatic CO2 reduction and dehalogenation are also described.

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References

  1. Tibrewal N, Tang Y (2014) Biocatalysts for natural product biosynthesis. Annu Rev Chem Biomol Eng 5:347–366. https://doi.org/10.1146/annurev-chembioeng-060713-040008

    Article  CAS  PubMed  Google Scholar 

  2. Devine PN, Howard RM, Kumar R, Thompson MP, Truppo MD, Turner NJ (2018) Extending the application of biocatalysis to meet the challenges of drug development. Nat Rev Chem 2(12):409–421. https://doi.org/10.1038/s41570-018-0055-1

    Article  Google Scholar 

  3. Taylor A, Heyes DJ, Scrutton NS (2022) Catalysis by Nature’s photoenzymes. Curr Opin Struct Biol 77:102491. https://doi.org/10.1016/j.sbi.2022.102491

    Article  CAS  PubMed  Google Scholar 

  4. Heyes DJ, Zhang S, Taylor A, Johannissen LO, Hardman SJO, Hay S, Scrutton NS (2021) Photocatalysis as the ‘master switch’ of photomorphogenesis in early plant development. Nat Plants 7(3):268–276. https://doi.org/10.1038/s41477-021-00866-5

    Article  CAS  PubMed  Google Scholar 

  5. Sancar A (2003) Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors. Chem Rev 103(6):2203–2237. https://doi.org/10.1021/cr0204348

    Article  CAS  PubMed  Google Scholar 

  6. Sorigue D, Legeret B, Cuine S, Blangy S, Moulin S, Billon E, Richaud P, Brugiere S, Coute Y, Nurizzo D, Muller P, Brettel K, Pignol D, Arnoux P, Li-Beisson Y, Peltier G, Beisson F (2017) An algal photoenzyme converts fatty acids to hydrocarbons. Science 357(6354):903–907. https://doi.org/10.1126/science.aan6349

    Article  CAS  PubMed  Google Scholar 

  7. Sorigue D, Hadjidemetriou K, Blangy S, Gotthard G, Bonvalet A, Coquelle N, Samire P, Aleksandrov A, Antonucci L, Benachir A, Boutet S, Byrdin M, Cammarata M, Carbajo S, Cuine S, Doak RB, Foucar L, Gorel A, Grunbein M, Hartmann E, Hienerwadel R, Hilpert M, Kloos M, Lane TJ, Legeret B, Legrand P, Li-Beisson Y, Moulin SLY, Nurizzo D, Peltier G, Schiro G, Shoeman RL, Sliwa M, Solinas X, Zhuang B, Barends TRM, Colletier JP, Joffre M, Royant A, Berthomieu C, Weik M, Domratcheva T, Brettel K, Vos MH, Schlichting I, Arnoux P, Muller P, Beisson F (2021) Mechanism and dynamics of fatty acid photodecarboxylase. Science 372(6538):148. https://doi.org/10.1126/science.abd5687

    Article  CAS  Google Scholar 

  8. Miller DC, Athavale SV, Arnold FH (2022) Combining chemistry and protein engineering for new-to-nature biocatalysis. Nat Synth 1(1):18–23. https://doi.org/10.1038/s44160-021-00008-x

    Article  PubMed  PubMed Central  Google Scholar 

  9. Lovelock SL, Crawshaw R, Basler S, Levy C, Baker D, Hilvert D, Green AP (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 

  10. Lee SH, Choi DS, Kuk SK, Park CB (2018) Photobiocatalysis: activating redox enzymes by direct or indirect transfer of photoinduced electrons. Angew Chem Int Ed Engl 57(27):7958–7985. https://doi.org/10.1002/anie.201710070

    Article  CAS  PubMed  Google Scholar 

  11. Hutton GA, Reuillard B, Martindale BC, Caputo CA, Lockwood CW, Butt JN, Reisner E (2016) Carbon dots as versatile photosensitizers for solar-driven catalysis with redox enzymes. J Am Chem Soc 138(51):16722–16730. https://doi.org/10.1021/jacs.6b10146

    Article  CAS  PubMed  Google Scholar 

  12. Kim J, Lee SH, Tieves F, Choi DS, Hollmann F, Paul CE, Park CB (2018) Biocatalytic C=C bond reduction through carbon nanodot-sensitized regeneration of NADH analogues. Angew Chem Int Ed Engl 57(42):13825–13828. https://doi.org/10.1002/anie.201804409

    Article  CAS  PubMed  Google Scholar 

  13. van Schie MMCH, Zhang W, Tieves F, Choi DS, Park CB, Burek BO, Bloh JZ, Arends IWCE, Paul CE, Alcalde M, Hollmann F (2019) Cascading g-C3N4 and peroxygenases for selective oxyfunctionalization reactions. ACS Catal 9(8):7409–7417. https://doi.org/10.1021/acscatal.9b01341

    Article  CAS  Google Scholar 

  14. Zhang SH, Shi JF, Sun YY, Wu YZ, Zhang YS, Cai ZY, Chen YX, You C, Han PP, Jiang ZY (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 

  15. Zhang SH, Shi JF, Chen YX, Huo Q, Li WR, Wu YZ, Sun YY, Zhang YS, Wang XD, Jiang ZY (2020) Unraveling and manipulating of NADH oxidation by photogenerated holes. ACS Catal 10(9):4967–4972. https://doi.org/10.1021/acscatal.0c00471

    Article  CAS  Google Scholar 

  16. Yadav RK, Baeg JO, Oh GH, Park NJ, Kong KJ, Kim J, Hwang DW, Biswas SK (2012) A photocatalyst-enzyme coupled artificial photosynthesis system for solar energy in production of formic acid from CO2. J Am Chem Soc 134(28):11455–11461. https://doi.org/10.1021/ja3009902

    Article  CAS  PubMed  Google Scholar 

  17. Yoon J, Lee SH, Tieves F, Rauch M, Hollmann F, Park CB (2019) Light-harvesting dye-alginate hydrogel for solar-driven, sustainable biocatalysis of asymmetric hydrogenation. ACS Sustain Chem Eng 7(6):5632–5637. https://doi.org/10.1021/acssuschemeng.9b01075

    Article  CAS  Google Scholar 

  18. Cesana PT, Li BX, Shepard SG, Ting SI, Hart SM, Olson CM, Alvarado JIM, Son MJ, Steiman TJ, Castellano FN, Doyle AG, MacMillan DWC, Schlau-Cohen GS (2022) A biohybrid strategy for enabling photoredox catalysis with low-energy light. Chem 8(1):174–185. https://doi.org/10.1016/j.chempr.2021.10.010

    Article  CAS  Google Scholar 

  19. Wang L, **e J, Schultz PG (2006) Expanding the genetic code. Annu Rev Biophys Biomol Struct 35:225–249. https://doi.org/10.1146/annurev.biophys.35.101105.121507

    Article  CAS  PubMed  Google Scholar 

  20. **e J, Schultz PG (2006) A chemical toolkit for proteins – an expanded genetic code. Nat Rev Mol Cell Biol 7(10):775–782. https://doi.org/10.1038/nrm2005

    Article  CAS  PubMed  Google Scholar 

  21. Liu CC, Schultz PG (2010) Adding new chemistries to the genetic code. Annu Rev Biochem 79:413–444. https://doi.org/10.1146/annurev.biochem.052308.105824

    Article  CAS  PubMed  Google Scholar 

  22. Hu C, Wang J (2016) Method for enzyme design with genetically encoded unnatural amino acids. In: Pecoraro VL (ed) Peptide, protein and enzyme design. Methods in enzymology, vol 580, pp 109–133. doi:https://doi.org/10.1016/bs.mie.2016.06.005

  23. Yu Y, Liu X, Wang J (2019) Expansion of redox chemistry in designer metalloenzymes. Acc Chem Res 52(3):557–565. https://doi.org/10.1021/acs.accounts.8b00627

    Article  CAS  PubMed  Google Scholar 

  24. Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H (2021) Recent advances in biocatalysis with chemical modification and expanded amino acid alphabet. Chem Rev 121(10):6173–6245. https://doi.org/10.1021/acs.chemrev.0c01201

    Article  CAS  PubMed  Google Scholar 

  25. Dorman G, Nakamura H, Pulsipher A, Prestwich GD (2016) The life of pi star: exploring the exciting and forbidden worlds of the benzophenone Photophore. Chem Rev 116(24):15284–15398. https://doi.org/10.1021/acs.chemrev.6b00342

    Article  CAS  PubMed  Google Scholar 

  26. Chin JW, Martin AB, King DS, Wang L, Schultz PG (2002) Addition of a photocrosslinking amino acid to the genetic code of Escherichiacoli. Proc Natl Acad Sci U S A 99(17):11020–11024. https://doi.org/10.1073/pnas.172226299

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Chin JW, Cropp TA, Anderson JC, Mukherji M, Zhang Z, Schultz PG (2003) An expanded eukaryotic genetic code. Science 301(5635):964–967. https://doi.org/10.1126/science.1084772

    Article  CAS  PubMed  Google Scholar 

  28. Hino N, Okazaki Y, Kobayashi T, Hayashi A, Sakamoto K, Yokoyama S (2005) Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid. Nat Methods 2(3):201–206. https://doi.org/10.1038/nmeth739

    Article  CAS  PubMed  Google Scholar 

  29. Coin I, Katritch V, Sun T, **ang Z, Siu FY, Beyermann M, Stevens RC, Wang L (2013) Genetically encoded chemical probes in cells reveal the binding path of urocortin-I to CRF class B GPCR. Cell 155(6):1258–1269. https://doi.org/10.1016/j.cell.2013.11.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Chen L, Zhu C, Guo H, Li R, Zhang L, **ng Z, Song Y, Zhang Z, Wang F, Liu X, Zhang Y, Ma RZ, Wang F (2020) Epitope-directed antibody selection by site-specific photocrosslinking. Sci Adv 6(14):eaaz7825. https://doi.org/10.1126/sciadv.aaz7825

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Mori H, Ito K (2006) Different modes of SecY-SecA interactions revealed by site-directed in vivo photo-cross-linking. Proc Natl Acad Sci U S A 103(44):16159–16164. https://doi.org/10.1073/pnas.0606390103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Bruninghoff K, Aust A, Taupitz KF, Wulff S, Dorner W, Mootz HD (2020) Identification of SUMO binding proteins enriched after covalent photo-cross-linking. ACS Chem Biol 15(9):2406–2414. https://doi.org/10.1021/acschembio.0c00609

    Article  CAS  PubMed  Google Scholar 

  33. Sun N, Huang J, Qian J, Zhou TP, Guo J, Tang L, Zhang W, Deng Y, Zhao W, Wu G, Liao RZ, Chen X, Zhong F, Wu Y (2022) Enantioselective [2+2]-cycloadditions with triplet photoenzymes. Nature 611(7937):715–720. https://doi.org/10.1038/s41586-022-05342-4

    Article  CAS  PubMed  Google Scholar 

  34. Trimble JS, Crawshaw R, Hardy FJ, Levy CW, Brown MJB, Fuerst DE, Heyes DJ, Obexer R, Green AP (2022) A designed photoenzyme for enantioselective [2+2] cycloadditions. Nature 611(7937):709–714. https://doi.org/10.1038/s41586-022-05335-3

    Article  CAS  PubMed  Google Scholar 

  35. Fu Y, Huang J, Wu Y, Liu X, Zhong F, Wang J (2021) Biocatalytic cross-coupling of aryl halides with a genetically engineered photosensitizer artificial dehalogenase. J Am Chem Soc 143(2):617–622. https://doi.org/10.1021/jacs.0c10882

    Article  CAS  PubMed  Google Scholar 

  36. Liu X, Kang F, Hu C, Wang L, Xu Z, Zheng D, Gong W, Lu Y, Ma Y, Wang J (2018) A genetically encoded photosensitizer protein facilitates the rational design of a miniature photocatalytic CO(2)-reducing enzyme. Nat Chem 10(12):1201–1206. https://doi.org/10.1038/s41557-018-0150-4

    Article  CAS  PubMed  Google Scholar 

  37. Kang F, Yu L, **a Y, Yu M, **a L, Wang Y, Yang L, Wang T, Gong W, Tian C, Liu X, Wang J (2021) Rational design of a miniature photocatalytic CO2-reducing enzyme. ACS Catal 11(9):5628–5635. https://doi.org/10.1021/acscatal.1c00287

    Article  CAS  Google Scholar 

  38. Tsien RY (1998) The green fluorescent protein. Annu Rev Biochem 67:509–544. https://doi.org/10.1146/annurev.biochem.67.1.509

    Article  CAS  PubMed  Google Scholar 

  39. Yang F, Moss LG, Phillips GN Jr (1996) The molecular structure of green fluorescent protein. Nat Biotechnol 14(10):1246–1251. https://doi.org/10.1038/nbt1096-1246

    Article  CAS  PubMed  Google Scholar 

  40. Pedelacq JD, Cabantous S, Tran T, Terwilliger TC, Waldo GS (2006) Engineering and characterization of a superfolder green fluorescent protein. Nat Biotechnol 24(1):79–88. https://doi.org/10.1038/nbt1172

    Article  CAS  PubMed  Google Scholar 

  41. Craggs TD (2009) Green fluorescent protein: structure, folding and chromophore maturation. Chem Soc Rev 38(10):2865–2875. https://doi.org/10.1039/b903641p

    Article  CAS  PubMed  Google Scholar 

  42. Kuehnel MF, Orchard KL, Dalle KE, Reisner E (2017) Selective photocatalytic CO2 reduction in water through anchoring of a molecular Ni catalyst on CdS nanocrystals. J Am Chem Soc 139(21):7217–7223. https://doi.org/10.1021/jacs.7b00369

    Article  CAS  PubMed  Google Scholar 

  43. Shields BJ, Doyle AG (2016) Direct C(sp(3))-H cross coupling enabled by catalytic generation of chlorine radicals. J Am Chem Soc 138(39):12719–12722. https://doi.org/10.1021/jacs.6b08397

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Dauter Z, Wilson KS, Sieker LC, Meyer J, Moulis JM (1997) Atomic resolution (0.94 A) structure of clostridium acidurici ferredoxin. Detailed geometry of [4Fe-4S] clusters in a protein. Biochemistry 36(51):16065–16073. https://doi.org/10.1021/bi972155y

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors are grateful to the National Key R&D Program of China (2021YFA0910802, 2019YFA0904002, 2019YFA0904103, 2020YFA0908503, 2020YFA0907701) and Sanming Project of Medicine in Shenzhen (no. SZSM201811092).

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Wang, J., **a, Y., Guo, X. (2023). Repurposing Photosensitizer Proteins Through Genetic Code Expansion to Facilitate Photo-Biocatalysis. In: Tsai, YH., Elsässer, S.J. (eds) Genetically Incorporated Non-Canonical Amino Acids. Methods in Molecular Biology, vol 2676. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3251-2_3

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  • DOI: https://doi.org/10.1007/978-1-0716-3251-2_3

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