Dr Yosephine Gumulya
FaBA Future Academic Leader in Precision Fermentation
School of Agriculture and Food Sustainability
Researcher biography
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.
Book Chapter
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 Articles
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
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, 104115. doi: 10.1016/j.resmic.2023.104115
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, 63 (18) e202314869, 1-10. doi: 10.1002/anie.202314869
Harris, Kurt L., Zhang, Yichi, Yang, Jade, Zeigler, Maxwell B., Thomson, Raine E. S., Carrera-Pacheco, Saskya E., Russell, Drake, Okada, Shoko, Strohmaier, Silja J., Gumulya, Yosephine, Scott, Colin, Totah, Rheem A. and Gillam, Elizabeth M. J. (2024). Thermostable fatty acid hydroxylases from ancestral reconstruction of cytochrome P450 family 4 enzymes. Catalysis Science & Technology, 14 (15), 4211-4227. doi: 10.1039/d4cy00090k
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, 1-11. doi: 10.1038/s41467-023-37070-2
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
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
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
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
Gumulya, Yosephine, Zea, Luis and Kaksonen, Anna H. (2022). In situ resource utilisation: The potential for space biomining. Minerals Engineering, 176 107288, 1-12. doi: 10.1016/j.mineng.2021.107288
Kaksonen, Anna H., Deng, Xiao, Morris, Christina, Khaleque, Himel Nahreen, Zea, Luis and Gumulya, Yosephine (2021). Potential of acidithiobacillus ferrooxidans to grow on and bioleach metals from mars and lunar regolith simulants under simulated microgravity conditions. Microorganisms, 9 (12) 2416, 2416. doi: 10.3390/microorganisms9122416
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
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
Gumulya, Yosephine, Boxall, Naomi J., Khaleque, Himel N., Santala, Ville, Carlson, Ross P. and Kaksonen, Anna H. (2018). In a quest for engineering acidophiles for biomining applications: Challenges and opportunities. Genes, 9 (2) 116, 116. doi: 10.3390/genes9020116
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
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
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
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
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
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
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
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
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
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
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
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