Back to the future: Why we need enzymology to build a synthetic metabolism of the future

Scholarly Works

• Farfán, D.; Gómez-Márquez, C.; Sandoval-Nuñez, D.; Paredes, O.; Morales, J. A. BARTReact: SELFIES-driven precision in reaction modeling. Franklin Open 2024, 7, 100106. doi:10.1016/j.fraope.2024.100106
• Sun, Y.; Tang, Y.; Zhou, J.; Guo, B.; Yuan, F.; Yao, B.; Yu, Y.; Li, C. Computational design of myoglobin-based carbene transferases for monoterpene derivatization. Biochemical and biophysical research communications 2024, 722, 150160. doi:10.1016/j.bbrc.2024.150160
• Yuan, F.; Ding, J.; Sun, Y.; Liang, J.; Luo, Y.; Yu, Y. Synthesis of Trifluoromethylated Monoterpenes by an Engineered Cytochrome P450. Chemistry (Weinheim an der Bergstrasse, Germany) 2024, 30, e202302936. doi:10.1002/chem.202302936
• Joshi, J.; Hanson, A. D. A pilot oral history of plant synthetic biology. Plant physiology 2024, 195, 36–47. doi:10.1093/plphys/kiad585
• Yang, X.; Zhang, Y.; Zhao, G. Artificial carbon assimilation: From unnatural reactions and pathways to synthetic autotrophic systems. Biotechnology advances 2023, 70, 108294. doi:10.1016/j.biotechadv.2023.108294
• Shebek, K. M.; Strutz, J.; Broadbelt, L. J.; Tyo, K. E. J. Pickaxe: a Python library for the prediction of novel metabolic reactions. BMC bioinformatics 2023, 24, 106. doi:10.1186/s12859-023-05149-8
• Tan, Z.; Li, J.; Hou, J.; Gonzalez, R. Designing artificial pathways for improving chemical production. Biotechnology advances 2023, 64, 108119. doi:10.1016/j.biotechadv.2023.108119
• Liew, F. E.; Nogle, R.; Abdalla, T.; Rasor, B. J.; Canter, C.; Jensen, R. O.; Wang, L.; Strutz, J.; Chirania, P.; De Tissera, S.; Mueller, A. P.; Ruan, Z.; Gao, A.; Tran, L.; Engle, N. L.; Bromley, J. C.; Daniell, J.; Conrado, R.; Tschaplinski, T. J.; Giannone, R. J.; Hettich, R. L.; Karim, A. S.; Simpson, S. D.; Brown, S. D.; Leang, C.; Jewett, M. C.; Köpke, M. Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale. Nature biotechnology 2022, 40, 335–344. doi:10.1038/s41587-021-01195-w
• Pavan, M.; Reinmets, K.; Garg, S.; Mueller, A. P.; Marcellin, E.; Köpke, M.; Valgepea, K. Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy. Metabolic engineering 2022, 71, 117–141. doi:10.1016/j.ymben.2022.01.015
• Motto, M.; Sahay, S. Energy plants (crops): potential natural and future designer plants. Handbook of Biofuels; Elsevier, 2022; pp 73–114. doi:10.1016/b978-0-12-822810-4.00004-x
• Rembeza, E.; Engqvist, M. K. M. Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class. PLoS computational biology 2021, 17, e1009446. doi:10.1371/journal.pcbi.1009446
• Löwe, H.; Kremling, A. In-Depth Computational Analysis of Natural and Artificial Carbon Fixation Pathways. Biodesign research 2021, 2021, 1–23. doi:10.34133/2021/9898316
• Barati, B.; Zeng, K.; Baeyens, J.; Wang, S.; Addy, M.; Gan, S. Y.; Abomohra, A. E.-F. Recent progress in genetically modified microalgae for enhanced carbon dioxide sequestration. Biomass and Bioenergy 2021, 145, 105927. doi:10.1016/j.biombioe.2020.105927
• Rasor, B. J.; Vögeli, B.; Landwehr, G. M.; Bogart, J. W.; Karim, A. S.; Jewett, M. C. Toward sustainable, cell-free biomanufacturing. Current opinion in biotechnology 2021, 69, 136–144. doi:10.1016/j.copbio.2020.12.012
• Löwe, H.; Kremling, A. In-depth computational analysis of natural and artificial carbon fixation pathways. Cold Spring Harbor Laboratory 2021. doi:10.1101/2021.01.05.425423
• Scheffen, M.; Marchal, D. G.; Beneyton, T.; Schuller, S. K.; Klose, M.; Diehl, C.; Lehmann, J.; Pfister, P.; Carrillo, M.; He, H.; Aslan, S.; Cortina, N. S.; Claus, P.; Bollschweiler, D.; Baret, J.-C.; Schuller, J. M.; Zarzycki, J.; Bar-Even, A.; Erb, T. J. A new-to-nature carboxylation module to improve natural and synthetic CO2 fixation. Nature Catalysis 2021, 4, 105–115. doi:10.1038/s41929-020-00557-y
• Rembeza, E.; Engqvist, M. K. M. Experimental investigation of enzyme functional annotations reveals extensive annotation error. Cold Spring Harbor Laboratory 2020. doi:10.1101/2020.12.18.423474
• Kemp, L.; Adam, L.; Boehm, C. R.; Breitling, R.; Casagrande, R.; Dando, M.; Djikeng, A.; Evans, N.; Hammond, R.; Hills, K.; Holt, L. A.; Kuiken, T.; Markotić, A.; Millett, P.; Napier, J. A.; Nelson, C.; ÓhÉigeartaigh, S. S.; Osbourn, A.; Palmer, M. J.; Patron, N. J.; Perello, E.; Piyawattanametha, W.; Restrepo-Schild, V.; Rios-Rojas, C.; Rhodes, C.; Roessing, A.; Scott, D.; Shapira, P.; Simuntala, C.; Smith, R. D.; Sundaram, L. S.; Takano, E.; Uttmark, G.; Wintle, B. C.; Zahra, N. B.; Sutherland, W. J. Bioengineering horizon scan 2020. eLife 2020, 9. doi:10.7554/elife.54489
• Niehaus, T. D.; Hillmann, K. B. Enzyme promiscuity, metabolite damage, and metabolite damage control systems of the tricarboxylic acid cycle. The FEBS journal 2020, 287, 1343–1358. doi:10.1111/febs.15284
• Batista-Silva, W.; da Fonseca-Pereira, P.; Martins, A. O.; Zsögön, A.; Nunes-Nesi, A.; Araújo, W. L. Engineering Improved Photosynthesis in the Era of Synthetic Biology. Plant communications 2020, 1, 100032. doi:10.1016/j.xplc.2020.100032

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