Overview
Background
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.
Availability
- Dr Yosephine Gumulya is:
- Available for supervision
Qualifications
- Doctor of Philosophy of Natural Sciences, Ruhr University Bochum
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.
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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.
Works
Search Professor Yosephine Gumulya’s works on UQ eSpace
2025
Journal Article
Isolation of an exopolysaccharide-producing Weissella confusa strain from lettuce and exploring its application as a texture modifying adjunct culture in a soy milk alternative
Huang, Wenkang, Yang, Shuyu, Wätjen, Anders Peter, Gumulya, Yosephine, Fernández-Pacheco, Pilar, Marcellin, Esteban, Prakash, Sangeeta, Bang-Berthelsen, Claus Heiner and Turner, Mark S. (2025). Isolation of an exopolysaccharide-producing Weissella confusa strain from lettuce and exploring its application as a texture modifying adjunct culture in a soy milk alternative. International Journal of Food Microbiology, 428 110992, 110992. doi: 10.1016/j.ijfoodmicro.2024.110992
2024
Journal Article
Ancestral sequence reconstruction reveals determinants of regioselectivity in C(sp3)-H oxyfunctionalization reactions by CYP505Es
Ebrecht, Ana C., Aschenbrenner, Jasmin C., Gumulya, Yosephine, Smit, Martha S. and Opperman, Diederik J. (2024). Ancestral sequence reconstruction reveals determinants of regioselectivity in C(sp3)-H oxyfunctionalization reactions by CYP505Es. ACS Catalysis, 15 (1), 595-600. doi: 10.1021/acscatal.4c06260
2024
Journal Article
Thermostable fatty acid hydroxylases from ancestral reconstruction of cytochrome P450 family 4 enzymes
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
2024
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
2024
Journal Article
Simulating compatible solute biosynthesis using a metabolic flux model of the biomining acidophile, Acidithiobacillus ferrooxidans ATCC 23270
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) 104115, 1-9. doi: 10.1016/j.resmic.2023.104115
2024
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, 63 (18) e202314869, 1-10. doi: 10.1002/anie.202314869
2023
Journal Article
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, 1-11. doi: 10.1038/s41467-023-37070-2
2022
Journal Article
Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)
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
2022
Journal Article
Ancestral sequence reconstruction of the CYP711 family reveals functional divergence in strigolactone biosynthetic enzymes associated with gene duplication events in monocot grasses
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
2022
Journal Article
Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defense reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebrates
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
2022
Journal Article
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
2022
Journal Article
In situ resource utilisation: The potential for space biomining
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
2021
Journal Article
Potential of Acidithiobacillus ferrooxidans to grow on and bioleach metals from Mars and lunar regolith simulants under simulated microgravity conditions
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, 1-16. doi: 10.3390/microorganisms9122416
2020
Conference Publication
APIS: Applications And Potentials Of Intelligent Swarms for magnetospheric studies
Rajan, Raj Thilak, Ben-Maor, Shoshana, Kaderali, Shaziana, Turner, Calum, Haken, Dawn, Paul, Gary, Vedant,, Melograna, Catrina, Salmeri, Antonino, Sreekumar, V., Weppler, Johannes, Gumulya, Yosephine, Milhim, Mohammed, Bunt, Riccardo, Bulgarini, Asia, Marnat, Maurice, Bussov, Kadri, Pringle, Frederick, Ma, Jusha, Amrutkar, Rushanka, Coto, Miguel, He, Jiang, Shi, Zijian, Hayder, Shahd-Lilly, Jaber, Dina Saad Fayez, Zuo, Junchao, Alsukour, Mohammad, Renaud, Cécile, Christie, Matthew ... Cohen, Jacob (2020). APIS: Applications And Potentials Of Intelligent Swarms for magnetospheric studies. 71st International Astronautical Congress, Virtual, 12-14 October 2020. Oxford, United Kingdom: International Astronautical Federation.
2020
Journal Article
Prospective directions for biohydrometallurgy
Kaksonen, Anna H., Deng, Xiao, Bohu, Tsing, Zea, Luis, Khaleque, Himel Nahreen, Gumulya, Yosephine, Boxall, Naomi J., Morris, Christina and Cheng, Ka Yu (2020). Prospective directions for biohydrometallurgy. Hydrometallurgy, 195 105376, 1-17. doi: 10.1016/j.hydromet.2020.105376
2019
Journal Article
Engineering thermostable CYP2D enzymes for biocatalysis using combinatorial libraries of ancestors for directed evolution (CLADE)
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
2018
Journal Article
Urban mining of lithium-ion batteries in Australia: Current state and future trends
Boxall, Naomi J., King, Sarah, Cheng, Ka Yu, Gumulya, Yosephine, Bruckard, Warren and Kaksonen, Anna H. (2018). Urban mining of lithium-ion batteries in Australia: Current state and future trends. Minerals Engineering, 128, 45-55. doi: 10.1016/j.mineng.2018.08.030
2018
Journal Article
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
2018
Journal Article
Recent progress in biohydrometallurgy and microbial characterisation
Kaksonen, Anna H., Boxall, Naomi J., Gumulya, Yosephine, Khaleque, Himel N., Morris, Christina, Bohu, Tsing, Cheng, Ka Yu, Usher, Kayley M. and Lakaniemi, Aino-Maija (2018). Recent progress in biohydrometallurgy and microbial characterisation. Hydrometallurgy, 180, 7-25. doi: 10.1016/j.hydromet.2018.06.018
2018
Journal Article
In a quest for engineering acidophiles for biomining applications: Challenges and opportunities
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, 116-2. doi: 10.3390/genes9020116
Funding
Current funding
Supervision
Availability
- Dr Yosephine Gumulya is:
- Available for supervision
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Supervision history
Current supervision
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Doctor Philosophy
Optimizing Mixed Gas Fermentation for Enhanced Biofuel Production
Associate Advisor
Other advisors: Dr James Heffernan, Professor Esteban Marcellin
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Doctor Philosophy
Tailoring starter cultures for plant based dairy alternatives
Associate Advisor
Other advisors: Associate Professor Sangeeta Prakash, Professor Mark Turner
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Doctor Philosophy
Enhancing fermentations by smart starter culture selection
Associate Advisor
Other advisors: Professor Mark Turner
Completed supervision
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2019
Doctor Philosophy
Computational Modelling of Enzymes: Predicting and Understanding the Selectivity of an Epoxide Hydrolase
Associate Advisor
Other advisors: Professor Mikael Boden
Media
Enquiries
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