FaBA Future Academic Leader in Prec
Overview
Yosephine Gumulya has a degree in Food Technology (2004) from Bogor Agricultural University (Indonesia) and a Master of Biotechnology (2007) from Technical University Hamburg Harburg (Germany). She completed her PhD in 2010 at Max Planck Institute for Coal Research (Germany), where she learned how to mimic the natural evolution in laboratory and use this technique to generate novel enzymes for biotechnology applications. After spending 1.5 years working for food industry in Spain, in October 2012, she decided to pursue an academic career by doing postdoctoral research in the lab of Prof Elizabeth Gillam and A.Prof. Mikael Boden. Her research has focused on protein engineering and ancestral sequence reconstruction. This knowledge is essential for understanding the protein evolutionary histroy as well for creating robust yet promiscous enzymes for industrial applications.
Research Interests
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Ancestral protein reconstruction
Hypothesising that the Earth was hot in ancient times, resurrecting ancestral proteins in the laboratory can generate robust proteins that useful for industrial applications. -
Protein Engineering / Directed evolution
Mimicking the natural evolution in the laboratory can create biocatalysts with suitable properties for industrial applications (e.g. selectivity, activity, stability)
Research Impacts
A major limitation of industrial process development is the lack of robust enzymes with novel functions or suitable properties for industrial application. With laboratory-based methods (protein engineering and ancestral sequence reconstruction), we have generated stable yet promiscuous enzymes that can be used to generate drug metabolites. As a result, it will significantly speed up the drug development pipeline and, more importantly, reduce the cost of overall drug discovery process.
Qualifications
- Doctor of Philosophy, Ruhr University Bochum
Publications
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Journal Article: Engineering Biocatalysts for the C−H Activation of Fatty Acids by Ancestral Sequence Reconstruction**
Jones, Bethan S., Ross, Connie M., Foley, Gabriel, Pozhydaieva, Nadiia, Sharratt, Joseph W., Kress, Nico, Seibt, Lisa S., Thomson, Raine E. S., Gumulya, Yosephine, Hayes, Martin A., Gillam, Elizabeth M. J. and Flitsch, Sabine L. (2024). Engineering Biocatalysts for the C−H Activation of Fatty Acids by Ancestral Sequence Reconstruction**. Angewandte Chemie, 136 (18). doi: 10.1002/ange.202314869
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Khaleque, Himel Nahreen, Nazem-Bokaee, Hadi, Gumulya, Yosephine, Carlson, Ross P. and Kaksonen, Anna H. (2024). Simulating compatible solute biosynthesis using a metabolic flux model of the biomining acidophile, Acidithiobacillus ferrooxidans ATCC 23270. Research in Microbiology, 175 (1-2) ARTN 104115. doi: 10.1016/j.resmic.2023.104115
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Journal Article: Engineering Biocatalysts for the C‐H Activation of Fatty Acids by Ancestral Sequence Reconstruction
Jones, Bethan S., Ross, Connie M., Foley, Gabriel, Pozhydaieva, Nadiia, Sharratt, Joseph W., Kress, Nico, Seibt, Lisa S., Thomson, Raine E. S., Gumulya, Yosephine, Hayes, Martin A., Gillam, Elizabeth M. J. and Flitsch, Sabine (2024). Engineering Biocatalysts for the C‐H Activation of Fatty Acids by Ancestral Sequence Reconstruction. Angewandte Chemie International Edition, e202314869. doi: 10.1002/anie.202314869
Publications
Book Chapter
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Computational tools for directed evolution: a comparison of prospective and retrospective strategies
Zaugg, Julian, Gumulya, Yosephine, Gillam, Elizabeth M. J. and Bodén, Mikael (2014). Computational tools for directed evolution: a comparison of prospective and retrospective strategies. Directed evolution library creation: methods and protocols. (pp. 315-333) edited by Elizabeth M. J. Gillam, Janine N. Copp and David F. Ackerley. New York, NY, United States: Humana Press. doi: 10.1007/978-1-4939-1053-3_21
Journal Article
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Jones, Bethan S., Ross, Connie M., Foley, Gabriel, Pozhydaieva, Nadiia, Sharratt, Joseph W., Kress, Nico, Seibt, Lisa S., Thomson, Raine E. S., Gumulya, Yosephine, Hayes, Martin A., Gillam, Elizabeth M. J. and Flitsch, Sabine L. (2024). Engineering Biocatalysts for the C−H Activation of Fatty Acids by Ancestral Sequence Reconstruction**. Angewandte Chemie, 136 (18). doi: 10.1002/ange.202314869
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Khaleque, Himel Nahreen, Nazem-Bokaee, Hadi, Gumulya, Yosephine, Carlson, Ross P. and Kaksonen, Anna H. (2024). Simulating compatible solute biosynthesis using a metabolic flux model of the biomining acidophile, Acidithiobacillus ferrooxidans ATCC 23270. Research in Microbiology, 175 (1-2) ARTN 104115. doi: 10.1016/j.resmic.2023.104115
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Engineering Biocatalysts for the C‐H Activation of Fatty Acids by Ancestral Sequence Reconstruction
Jones, Bethan S., Ross, Connie M., Foley, Gabriel, Pozhydaieva, Nadiia, Sharratt, Joseph W., Kress, Nico, Seibt, Lisa S., Thomson, Raine E. S., Gumulya, Yosephine, Hayes, Martin A., Gillam, Elizabeth M. J. and Flitsch, Sabine (2024). Engineering Biocatalysts for the C‐H Activation of Fatty Acids by Ancestral Sequence Reconstruction. Angewandte Chemie International Edition, e202314869. doi: 10.1002/anie.202314869
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Toward sustainable space exploration: a roadmap for harnessing the power of microorganisms
Santomartino, Rosa, Averesch, Nils J. H., Bhuiyan, Marufa, Cockell, Charles S., Colangelo, Jesse, Gumulya, Yosephine, Lehner, Benjamin, Lopez-Ayala, Ivanna, McMahon, Sean, Mohanty, Anurup, Santa Maria, Sergio R., Urbaniak, Camilla, Volger, Rik, Yang, Jiseon and Zea, Luis (2023). Toward sustainable space exploration: a roadmap for harnessing the power of microorganisms. Nature Communications, 14 (1) 1391. doi: 10.1038/s41467-023-37070-2
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Foley, Gabriel, Mora, Ariane, Ross, Connie M., Bottoms, Scott, Sützl, Leander, Lamprecht, Marnie L., Zaugg, Julian, Essebier, Alexandra, Balderson, Brad, Newell, Rhys, Thomson, Raine E. S., Kobe, Bostjan, Barnard, Ross T., Guddat, Luke, Schenk, Gerhard, Carsten, Jörg, Gumulya, Yosephine, Rost, Burkhard, Haltrich, Dietmar, Sieber, Volker, Gillam, Elizabeth M. J. and Bodén, Mikael (2022). Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). PL o S Computational Biology, 18 (10) e1010633, e1010633. doi: 10.1371/journal.pcbi.1010633
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Vinde, Marcos H., Cao, Da, Chesterfield, Rebecca J., Yoneyama, Kaori, Gumulya, Yosephine, Thomson, Raine E. S., Matila, Tebogo, Ebert, Birgitta E., Beveridge, Christine A., Vickers, Claudia E. and Gillam, Elizabeth M. J. (2022). Ancestral sequence reconstruction of the CYP711 family reveals functional divergence in strigolactone biosynthetic enzymes associated with gene duplication events in monocot grasses. New Phytologist, 235 (5), 1900-1912. doi: 10.1111/nph.18285
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Harris, Kurt L., Thomson, Raine E.S., Gumulya, Yosephine, Foley, Gabriel, Carrera-Pacheco, Saskya E., Syed, Parnayan, Janosik, Tomasz, Sandinge, Ann-Sofie, Andersson, Shalini, Jurva, Ulrik, Bodén, Mikael and Gillam, Elizabeth M.J. (2022). Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defense reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebrates. Molecular Biology and Evolution, 39 (6) msac116. doi: 10.1093/molbev/msac116
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Applications and Potentials of Intelligent Swarms for magnetospheric studies
Rajan, Raj Thilak, Ben-Maor, Shoshana, Kaderali, Shaziana, Turner, Calum, Milhim, Mohammed, Melograna, Catrina, Haken, Dawn, Paul, Gary, Vedant, , Sreekumar, V., Weppler, Johannes, Gumulya, Yosephine, Bunt, Riccardo, Bulgarini, Asia, Marnat, Maurice, Bussov, Kadri, Pringle, Frederick, Ma, Jusha, Amrutkar, Rushanka, Coto, Miguel, He, Jiang, Shi, Zijian, Hayder, Shahd, Jaber, Dina Saad Fayez, Zuo, Junchao, Alsukour, Mohammad, Renaud, Cécile, Christie, Matthew, Engad, Neta ... Cohen, Jacob (2022). Applications and Potentials of Intelligent Swarms for magnetospheric studies. Acta Astronautica, 193, 554-571. doi: 10.1016/j.actaastro.2021.07.046
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<i>In</i><i> situ</i> resource utilisation: The potential for space biomining
Gumulya, Yosephine, Zea, Luis and Kaksonen, Anna H. (2021). In situ resource utilisation: The potential for space biomining. Minerals Engineering, 176 ARTN 107288. doi: 10.1016/j.mineng.2021.107288
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Gumulya, Yosephine, Huang, Weiliang, D'Cunha, Stephlina A., Richards, Katelyn E., Thomson, Raine E.S., Hunter, Dominic J.B., Baek, Jong-Min, Harris, Kurt L., Boden, Mikael, De Voss, James J., Hayes, Martin A., Isin, Emre M., Andersson, Shalini, Jurva, Ulrik and Gillam, Elizabeth (2019). Engineering thermostable CYP2D enzymes for biocatalysis using combinatorial libraries of ancestors for directed evolution (CLADE). ChemCatChem, 11 (2) cctc.201801644, 841-850. doi: 10.1002/cctc.201801644
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Engineering highly functional thermostable proteins using ancestral sequence reconstruction
Gumulya, Yosephin, Baek, Jong-Min, Wun, Shun-Jie, Thomson, Raine E. S., Harris, Kurt L., Hunter, Dominic J. B., Behrendorff, James B. Y. H., Kulig, Justyna, Zheng, Shan, Wu, Xueming, Wu, Bin, Stok, Jeanette E., De Voss, James J., Schenk, Gerhard, Jurva, Ulrik, Andersson, Shalini, Isin, Emre M., Bodén, Mikael, Guddat, Luke and Gillam, Elizabeth M. J. (2018). Engineering highly functional thermostable proteins using ancestral sequence reconstruction. Nature Catalysis, 1 (11), 878-888. doi: 10.1038/s41929-018-0159-5
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Effect of Binding on Enantioselectivity of Epoxide Hydrolase
Zaugg, Julian, Gumulya, Yosephine, Bodén, Mikael, Mark, Alan E and Malde, Alpeshkumar K (2018). Effect of Binding on Enantioselectivity of Epoxide Hydrolase. Journal of Chemical Information and Modeling, 58 (3), 630-640. doi: 10.1021/acs.jcim.7b00353
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Determinants of thermostability in the cytochrome P450 fold
Harris, Kurt L., Thomson, Raine E. S., Strohmaier, Silja J., Gumulya, Yosephine and Gillam, Elizabeth M. J. (2018). Determinants of thermostability in the cytochrome P450 fold. Biochimica et Biophysica Acta - Proteins and Proteomics, 1866 (1), 97-115. doi: 10.1016/j.bbapap.2017.08.003
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Learning epistatic interactions from sequence-activity data to predict enantioselectivity
Zaugg, Julian, Gumulya, Yosephine, Malde, Alpeshkumar K and Bodén, Mikael (2017). Learning epistatic interactions from sequence-activity data to predict enantioselectivity. Journal of computer-aided molecular design, 31 (12), 1085-1096. doi: 10.1007/s10822-017-0090-x
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Genetically programmed chiral organoborane synthesis
Jennifer Kan, S. B., Huang, Xiongyi, Gumulya, Yosephine, Chen, Kai and Arnold, Frances H. (2017). Genetically programmed chiral organoborane synthesis. Nature, 552 (7683), 132-136. doi: 10.1038/nature24996
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Gumulya, Yosephine and Gillam, Elizabeth M. J. (2016). Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the 'retro' approach to protein engineering. Biochemical Journal, 474 (1), 1-19. doi: 10.1042/BCJ20160507
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Many pathways in laboratory evolution can lead to improved enzymes: How to escape from local minima
Gumulya, Yosephine, Sanchis, Joaquin and Reetz, Manfred T. (2012). Many pathways in laboratory evolution can lead to improved enzymes: How to escape from local minima. ChemBioChem, 13 (7), 1060-1066. doi: 10.1002/cbic.201100784
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Gumulya, Yosephine and Reetz, Manfred T. (2011). Enhancing the thermal robustness of an enzyme by directed evolution: least favorable starting points and inferior mutants can map superior evolutionary Pathways. ChemBioChem, 12 (16), 2502-2510. doi: 10.1002/cbic.201100412
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Reetz, Manfred T., Soni, Pankaj, Fernandez, Layla, Gumulya, Yosephine and Carballeira, Jose D. (2010). Increasing the stability of an enzyme toward hostile organic solvents by directed evolution based on iterative saturation mutagenesis using the B-FIT method. Chemical Communications, 46 (45), 8657-8658. doi: 10.1039/c0cc02657c
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Reetz, Manfred T., Prasad, Shreenath, Carballeira, Jose D., Gumulya, Yosephine and Bocola, Marco (2010). Iterative saturation mutagenesis accelerates laboratory evolution of enzyme stereoselectivity: rigorous comparison with traditional methods. Journal of the American Chemical Society, 132 (26), 9144-9152. doi: 10.1021/ja1030479
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An efficient method for mutant library creation in Pichia pastoris useful in directed evolution
Fernandez, Layla, Jiao, Ning, Soni, Pankaj, Gumulya, Yosephine, De Oliveira, Luciana Gonzaga and Reetz, Manfred T. (2010). An efficient method for mutant library creation in Pichia pastoris useful in directed evolution. Biocatalysis and Biotransformation, 28 (2), 122-129. doi: 10.3109/10242420903505834
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Hollmann, Frank, Gumulya, Yosephine, Toelle, Christoph, Liese, Andreas and Thum, Oliver (2008). Evaluation of the laccase from Myceliophthora thermophila as industrial biocatalyst for polymerization reactions. Macromolecules, 41 (22), 8520-8524. doi: 10.1021/ma801763t
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Sanchis, Joaquin, Fernandez, Layla, Carballeira, J. Daniel, Drone, Jullien, Gumulya, Yosephine, Hoebenreich, Horst, Kahakeaw, Daniel, Kille, Sabrina, Lohmer, Renate, Peyralans, Jerome J. -P., Podtetenieff, John, Prasad, Shreenath, Soni, Pankaj, Taglieber, Andreas, Wu, Sheng, Zilly, Felipe E. and Reetz, Manfred T. (2008). Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates. Applied Microbiology and Biotechnology, 81 (2), 387-397. doi: 10.1007/s00253-008-1678-9
