The Quest for Xenobiotic Enzymes: From New Enzymes for Chemistry to a Novel Chemistry of Life.
artificial enzymes
biocatalysis
protein engineering
synthetic biology
xenobiology
Journal
Chembiochem : a European journal of chemical biology
ISSN: 1439-7633
Titre abrégé: Chembiochem
Pays: Germany
ID NLM: 100937360
Informations de publication
Date de publication:
17 08 2020
17 08 2020
Historique:
received:
28
02
2020
revised:
13
04
2020
pubmed:
16
4
2020
medline:
30
6
2021
entrez:
16
4
2020
Statut:
ppublish
Résumé
Enzyme engineering has made impressive progress in the past decades, paving the way for the widespread use of enzymes for various purposes. In contrast to "classical" enzyme engineering, which focuses on optimizing specific properties of natural enzymes, a more recent trend towards the creation of artificial enzymes that catalyze fundamentally distinct, new-to-nature reactions is observable. While approaches for creating such enzymes differ significantly, they share the common goal of enabling biocatalytic novelty to broaden the range of applications for enzymes. Although most artificial enzymes reported to date are only moderately active and barely function in vivo, they have the potential to endow cells with capabilities that were previously out of reach and thus herald a new wave of "functional xenobiology". Herein, we highlight recent developments in the field of artificial enzymes with a particular focus on challenges and opportunities for their use in xenobiology.
Identifiants
pubmed: 32294286
doi: 10.1002/cbic.202000121
doi:
Substances chimiques
Enzymes
0
Xenobiotics
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
2241-2249Informations de copyright
© 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Références
J. C. Lewis, P. S. Coelho, F. H. Arnold, Chem. Soc. Rev. 2011, 40, 2003-2021.
C. J. Li, B. M. Trost, Proc. Natl. Acad. Sci. USA 2008, 105, 13197-13202.
R. A. Sheldon, J. M. Woodley, Chem. Rev. 2018, 118, 801-838.
U. T. Bornscheuer, G. W. Huisman, R. J. Kazlauskas, S. Lutz, J. C. Moore, K. Robins, Nature 2012, 485, 185-194.
P. A. Romero, F. H. Arnold, Nat. Rev. Mol. Cell Biol. 2009, 10, 866-876.
K. Chen, F. H. Arnold, Proc. Natl. Acad. Sci. USA 1993, 90, 5618-5622.
W. P. C. Stemmer, Nature 1994, 370, 389-391.
S. Lutz, Curr. Opin. Biotechnol. 2010, 21, 734-743.
U. T. Bornscheuer, Philos. Trans. R. Soc. London 2018, 376, 20170063.
M. Jeschek, S. Panke, T. R. Ward, Trends Biotechnol. 2018, 36, 60-72.
M. Schmidt, BioEssays 2010, 32, 322-331.
V. B. Pinheiro, A. I. Taylor, C. Cozens, M. Abramov, M. Renders, S. Zhang, J. C. Chaput, J. Wengel, S.-Y. Peak-Chew, S. H. McLaughlin, P. Herdewijn, P. Holliger, Science 2012, 336, 341-344.
V. B. Pinheiro, P. Holliger, Curr. Opin. Chem. Biol. 2012, 16, 245-252.
J. W. Chin, Nature 2017, 550, 53-60.
P. S. Coelho, E. M. Brustad, A. Kannan, F. H. Arnold, Science 2013, 339, 307-310.
R. K. Zhang, K. Chen, X. Huang, L. Wohlschlager, H. Renata, F. H. Arnold, Nature 2019, 565, 67-72.
J. A. McIntosh, P. S. Coelho, C. C. Farwell, Z. J. Wang, J. C. Lewis, T. R. Brown, F. H. Arnold, Angew. Chem. Int. Ed. 2013, 52, 9309-9312;
Angew. Chem. 2013, 125, 9479-9482.
Y. Yang, I. Cho, X. Qi, P. Liu, F. H. Arnold, Nat. Chem. 2019, 11, 987-993.
C. K. Prier, R. K. Zhang, A. R. Buller, S. Brinkmann-Chen, F. H. Arnold, Nat. Chem. 2017, 9, 629-634.
M. Bordeaux, V. Tyagi, R. Fasan, Angew. Chem. Int. Ed. 2015, 54, 1744-1748;
Angew. Chem. 2015, 127, 1764-1768.
P. Bajaj, G. Sreenilayam, V. Tyagi, R. Fasan, Angew. Chem. Int. Ed. 2016, 55, 16110-16114;
Angew. Chem. 2016, 128, 16344-16348.
M. Bordeaux, R. Singh, R. Fasan, Bioorg. Med. Chem. 2014, 22, 5697-5704.
G. Sreenilayam, R. Fasan, Chem. Commun. 2015, 51, 1532-1534.
V. Tyagi, R. B. Bonn, R. Fasan, Chem. Sci. 2015, 6, 2488-2494.
S. B. J. Kan, R. D. Lewis, K. Chen, F. H. Arnold, Science 2016, 354, 1048-1051.
S. B. J. Kan, X. Huang, Y. Gumulya, K. Chen, F. H. Arnold, Nature 2017, 552, 132-136.
M. L. Matthews, W. C. Chang, A. P. Layne, L. A. Miles, C. Krebs, J. M. Bollinger, Nat. Chem. Biol. 2014, 10, 209-215.
C. K. Prier, F. H. Arnold, J. Am. Chem. Soc. 2015, 137, 13992-14006.
P. Dünkelmann, D. Kolter-Jung, A. Nitsche, A. S. Demir, P. Siegert, B. Lingen, M. Baumann, M. Pohl, M. Müller, J. Am. Chem. Soc. 2002, 124, 12084-12085.
E. Zandvoort, E. M. Geertsema, B. J. Baas, W. J. Quax, G. J. Poelarends, Angew. Chem. Int. Ed. 2012, 51, 1240-1243;
Angew. Chem. 2012, 124, 1266-1269.
M. A. Emmanuel, N. R. Greenberg, D. G. Oblinsky, T. K. Hyster, Nature 2016, 540, 414-417.
F. P. Guengerich, J. Biol. Chem. 2009, 284, 709-709.
J. C. Lewis, ACS Catal. 2013, 3, 2954-2975.
K. Oohora, Y. Kihira, E. Mizohata, T. Inoue, T. Hayashi, J. Am. Chem. Soc. 2013, 135, 17282-17285.
H. M. Key, P. Dydio, D. S. Clark, J. F. Hartwig, Nature 2016, 534, 534-537.
P. Dydio, H. M. Key, A. Nazarenko, J. Y.-E. Rha, V. Seyedkazemi, D. S. Clark, J. F. Hartwig, Science 2016, 354, 102-106.
P. Dydio, H. M. Key, H. Hayashi, D. S. Clark, J. F. Hartwig, J. Am. Chem. Soc. 2017, 139, 1750-1753.
J. Huang, Z. Liu, B. Bloomer, D. Clark, A. Mukhopadhyay, J. Keasling, J. Hartwig, ChemRxiv 2020, 1-11.
M. Jeschek, M. O. Bahls, V. Schneider, P. Marlière, T. R. Ward, S. Panke, Metab. Eng. 2017, 40, 33-40.
F. Schwizer, Y. Okamoto, T. Heinisch, Y. Gu, M. M. Pellizzoni, V. Lebrun, R. Reuter, V. Köhler, J. C. Lewis, T. R. Ward, Chem. Rev. 2018, 118, 142-231.
T. K. Hyster, L. Knorr, T. R. Ward, T. Rovis, Science 2012, 338, 500-503.
V. Köhler, Y. M. Wilson, M. Dürrenberger, D. Ghislieri, E. Churakova, T. Quinto, L. Knörr, D. Häussinger, F. Hollmann, N. J. Turner, T. R. Ward, Nat. Chem. 2013, 5, 93-99.
M. Jeschek, R. Reuter, T. Heinisch, C. Trindler, J. Klehr, S. Panke, T. R. Ward, Nature 2016, 537, 661-665.
J. Bos, W. R. Browne, A. J. M. Driessen, G. Roelfes, J. Am. Chem. Soc. 2015, 137, 9796-9799.
L. Villarino, K. E. Splan, E. Reddem, L. Alonso-Cotchico, C. Gutiérrez de Souza, A. Lledós, J. D. Maréchal, A. M. W. H. Thunnissen, G. Roelfes, Angew. Chem. Int. Ed. 2018, 57, 7785-7789;
Angew. Chem. 2018, 130, 7911-7915.
J. Bos, A. García-Herraiz, G. Roelfes, Chem. Sci. 2013, 4, 3578-3582.
I. Drienovská, A. Rioz-Martínez, A. Draksharapu, G. Roelfes, Chem. Sci. 2015, 6, 770-776.
I. Drienovská, L. Alonso-Cotchico, P. Vidossich, A. Lledós, J. D. Maréchal, G. Roelfes, Chem. Sci. 2017, 8, 7228-7235.
N. Ségaud, I. Drienovská, J. Chen, W. R. Browne, G. Roelfes, Inorg. Chem. 2017, 56, 13293-13299.
H. Yang, P. Srivastava, C. Zhang, J. C. Lewis, ChemBioChem 2014, 15, 223-227.
P. Srivastava, H. Yang, K. Ellis-Guardiola, J. C. Lewis, Nat. Commun. 2015, 6, 1-8.
H. Yang, A. M. Swartz, H. J. Park, P. Srivastava, K. Ellis-Guardiola, D. M. Upp, G. Lee, K. Belsare, Y. Gu, C. Zhang, R. E. Moellering, J. C. Lewis, Nat. Chem. 2018, 10, 318-324.
F. Agostini, J. S. Völler, B. Koksch, C. G. Acevedo-Rocha, V. Kubyshkin, N. Budisa, Angew. Chem. Int. Ed. 2017, 56, 9680-9703;
Angew. Chem. 2017, 129, 9810-9835.
E. N. Mirts, A. Bhagi-Damodaran, Y. Lu, Acc. Chem. Res. 2019, 52, 935-944.
I. Drienovská, C. Mayer, C. Dulson, G. Roelfes, Nat. Chem. 2018, 10, 946-952.
J. B. Siegel, A. Zanghellini, H. M. Lovick, G. Kiss, A. R. Lambert, J. L. St. Clair, J. L. Gallaher, D. Hilvert, M. H. Gelb, B. L. Stoddard, K. N. Houk, F. E. Michael, D. Baker, Science 2010, 329, 309-313.
S. Studer, S. L. Guffy, B. S. Der, A. Debon, Z. L. Pianowski, D. A. Hansen, B. Kuhlman, P. R. E. Mittl, D. Hilvert, Science 2018, 362, 1285-1288.
C. C. Liu, P. G. Schultz, Annu. Rev. Biochem. 2010, 79, 413-444.
T. Hayashi, M. Tinzl, T. Mori, U. Krengel, J. Proppe, J. Soetbeer, D. Klose, G. Jeschke, M. Reiher, D. Hilvert, Nat. Can. 2018, 1, 578-584.
C. Mayer, C. Dulson, E. Reddem, A. M. W. H. Thunnissen, G. Roelfes, Angew. Chem. Int. Ed. 2019, 58, 2083-2087.
Z. Zhou, G. Roelfes, Nat. Can. 2020, 3, DOI 10.1038/s41929-019-0420-6.
A. J. Burke, S. L. Lovelock, A. Frese, R. Crawshaw, M. Ortmayer, M. Dunstan, C. Levy, A. P. Green, Nature 2019, 570, 219-223.
P.-S. Huang, S. E. Boyken, D. Baker, Nature 2016, 537, 320-327.
V. Vaissier Welborn, T. Head-Gordon, Chem. Rev. 2019, 119, 6613-6630.
D. Röthlisberger, O. Khersonsky, A. M. Wollacott, L. Jiang, J. DeChancie, J. Betker, J. L. Gallaher, E. A. Althoff, A. Zanghellini, O. Dym, S. Albeck, K. N. Houk, D. S. Tawfik, D. Baker, Nature 2008, 453, 190-195.
L. Jiang, E. A. Althoff, F. R. Clemente, L. Doyle, D. Röthlisberger, A. Zanghellini, J. L. Gallaher, J. L. Betker, F. Tanaka, C. F. Barbas, D. Hilvert, K. N. Houk, B. L. Stoddard, D. Baker, Science 2008, 319, 1387-1391.
A. Bar-Even, E. Noor, Y. Savir, W. Liebermeister, D. Davidi, D. S. Tawfik, R. Milo, Biochemistry 2011, 50, 4402-4410.
O. Khersonsky, G. Kiss, D. Röthlisberger, O. Dym, S. Albeck, K. N. Houk, D. Baker, D. S. Tawfik, Proc. Natl. Acad. Sci. USA 2012, 109, 10358-10363.
R. Blomberg, H. Kries, D. M. Pinkas, P. R. E. Mittl, M. G. Grütter, H. K. Privett, S. L. Mayo, D. Hilvert, Nature 2013, 503, 418-421.
V. Vaissier, S. C. Sharma, K. Schaettle, T. Zhang, T. Head-Gordon, ACS Catal. 2018, 8, 219-227.
E. A. Althoff, L. Wang, L. Jiang, L. Giger, J. K. Lassila, Z. Wang, M. Smith, S. Hari, P. Kast, D. Herschlag, D. Hilvert, D. Baker, Protein Sci. 2012, 21, 717-726.
L. Giger, S. Caner, R. Obexer, P. Kast, D. Baker, N. Ban, D. Hilvert, Nat. Chem. Biol. 2013, 9, 494-498.
R. Obexer, A. Godina, X. Garrabou, P. R. E. Mittl, D. Baker, A. D. Griffiths, D. Hilvert, Nat. Chem. 2017, 9, 50-56.
J. B. Siegel, A. L. Smith, S. Poust, A. J. Wargacki, A. Bar-Even, C. Louw, B. W. Shen, C. B. Eiben, H. M. Tran, E. Noor, J. L. Gallaher, J. Bale, Y. Yoshikuni, M. H. Gelb, J. D. Keasling, B. L. Stoddard, M. E. Lidstrom, D. Baker, Proc. Natl. Acad. Sci. USA 2015, 112, 3704-3709.
K. Johnsson, R. K. Allemann, H. Widmer, S. A. Benner, Nature 1993, 365, 530-532.
A. J. Burton, A. R. Thomson, W. M. Dawson, R. L. Brady, D. N. Woolfson, Nat. Chem. 2016, 8, 837-844.
M. L. Zastrow, A. F. A. Peacock, J. A. Stuckey, V. L. Pecoraro, Nat. Chem. 2012, 4, 118-123.
V. M. Cangelosi, A. Deb, J. E. Penner-Hahn, V. L. Pecoraro, Angew. Chem. Int. Ed. 2014, 53, 7900-7903;
Angew. Chem. 2014, 126, 8034-8037.
W. J. Song, F. A. Tezcan, Science 2014, 346, 1525-1528.
R. Stenner, J. W. Steventon, A. Seddon, J. L. R. Anderson, Proc. Natl. Acad. Sci. USA 2020, 117, 1419-1428.
Y. M. Wilson, M. Dürrenberger, E. S. Nogueira, T. R. Ward, J. Am. Chem. Soc. 2014, 136, 8928-8932.
M. Martínez-Calvo, J. L. Mascareñas, Coord. Chem. Rev. 2018, 359, 57-79.
J. G. Rebelein, T. R. Ward, Curr. Opin. Biotechnol. 2018, 53, 106-114.
T. Heinisch, F. Schwizer, B. Garabedian, E. Csibra, M. Jeschek, J. Vallapurackal, V. B. Pinheiro, P. Marlière, S. Panke, T. R. Ward, Chem. Sci. 2018, 9, 5383-5388.
W. Ghattas, V. Dubosclard, A. Wick, A. Bendelac, R. Guillot, R. Ricoux, J. P. Mahy, J. Am. Chem. Soc. 2018, 140, 8756-8762.
T. Kuenzl, M. Sroka, P. Srivastava, P. Herdewijn, P. Marlière, S. Panke, Metab. Eng. 2017, 39, 60-70.
J. J. Woodward, N. I. Martin, M. A. Marletta, Nat. Methods 2007, 4, 43-45.
E. W. Reynolds, M. W. McHenry, F. Cannac, J. G. Gober, C. D. Snow, E. M. Brustad, J. Am. Chem. Soc. 2016, 138, 12451-12458.
A. E. Donnelly, G. S. Murphy, K. M. Digianantonio, M. H. Hecht, Nat. Chem. Biol. 2018, 14, 253-255.
I. V. Korendovych, W. F. DeGrado, Curr. Opin. Struct. Biol. 2014, 27, 113-121.
T. J. Erb, P. R. Jones, A. Bar-Even, Curr. Opin. Chem. Biol. 2017, 37, 56-62.