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Professor Elizabeth Gillam

Professor

School of Chemistry and Molecular Biosciences
Faculty of Science
e.gillam@uq.edu.au
+61 7 336 51410

Overview

The molecular evolution of cytochrome P450 Enzymes: biological catalysts of unprecedented versatility.

Cytochrome P450 enzymes (CYPs, P450s) especially those responsible for drug metabolism in humans, are the unifying theme of the research in our lab. These fascinating enzymes are catalysts of exceptional versatility, and functional diversity. In humans they are principally responsible for the clearance of a practically unlimited variety of chemicals from the body, but are also critical in many important physiological processes. In other organisms (plants, animals, bacteria, fungi, almost everything!) they carry out an unprecedented range of functions, such as defense, chemical communication, neural development and even pigmentation. P450s are involved in the biosynthesis of an unequalled range of potent, biologically active natural products in microbes, plants and animals, including many antibiotics, plant and animal hormones, signalling molecules, toxins, flavours and fragrances. We are studying how P450s have evolved to deal with novel substrates by reconstructing ancestral precursors and evolutionary pathways, to answer such questions as how did the koala evolve to live on eucalyptus leaves, a toxic diet for most mammals.

The capabilities of P450s are only just coming to be fully recognized and structural studies on P450s should yield critical insights into how enzyme structure determines function. For example, recently we discovered that P450s are present within cells in the Fe(II) form, a finding that has led to a radical revision of the dogma concerning the P450 catalytic cycle, and has implications for the control of uncoupling of P450 activity in cells. Importantly, the biotechnological potential of P450s remains yet to be exploited. All of the specific research themes detailed below take advantage of our recognized expertise in the expression of recombinant human cytochrome P450 enzymes in bacteria. Our group is interested in finding out how P450s work and how they can be made to work better.

Artificial evolution of P450s for drug development and bioremediation: a way of exploring the sequence space and catalytic potential of P450s. The demonstrated catalytic diversity of P450 enzymes makes them the ideal starting material for engineering sophisticated chemical reagents to catalyse difficult chemical transformations. We are using artificial (or directed) evolution to engineer enzymes that are more efficient, robust and specialized than naturally occurring enzymes with the aim of selecting for properties that are commercially useful in the areas of drug discovery and development and bioremediation of pollutants in the environment. The approach we are using also allows us to explore the essential sequence and structural features that underpin all ~12000 known P450s so as to determine how they work.

Synthetic biology of enzymes for clean, green, solar-powered chemistry in drug development, bioremediation and biosensors. We have identified ancestral enzymes that are extremely thermostable compared to their modern counterparts, making them potentially very useful in industry, since they can withstand long incubations at elevated temperatures. They can be used as ‘off the shelf’ reagents to catalyse useful chemistry, such as in in drug discovery and development, fine chemicals synthesis, and cleaning up the environment. Working with drug companies, we are exploring how they can be best deployed in chemical processes and what structural features make them efficient, robust and specialized. We are also immobilizing P450s in virus-like-particles as ‘designer’ reagents that can be recovered from reactions and reused. To make such processes cheaper and more sustainable, we are using photosynthesis to power P450 reactions for clean, green biocatalysis in microalgae.

Biosketch:

After graduating from UQ with first class Honours in Biochemistry, Elizabeth took up a Royal Commission for the Exhibition of 1851 Overseas Scholarship to pursue doctoral work at Oxford University then undertook postdoctoral work at the Center in Molecular Toxicology and Department of Biochemistry at Vanderbilt University School of Medicine with Prof. F.P. Guengerich. She returned to UQ in 1993 to take up a position in Pharmacology and joined the School of Chemistry and Molecular Biosciences in 2009 as a Professor of Biochemistry.

Research Interests

  • Synthetic Biology
    We are developing novel systems for biocatalysis to replace energy-intensive steps in chemical processes, such as in the synthesis of drugs, with more sustainable alternatives using enzymes. We are engineering cytochrome P450 enzymes as biocatalysts, attaching them to protein cages and linking them to photosynthesis as a green energy source.
  • Molecular evolution
    Plants and the animals that consume them are locked in an evolutionary battle involving chemical warfare: plants produce toxins to discourage animals from eating them and in turn, animals develop enzymes to metabolise the plant toxins. We are studying the way enzymes in animals have evolved to respond to the changing chemical environment presented by plant secondary metabolism, processes that have a direct bearing on the ability of people to metabolise drugs and other environmental chemicals.
  • Protein engineering
    Enzymes such as cytochromes P450 are powerful, specific catalysts that could be very useful in making chemical industries more sustainable and environmentally benign. However naturally occurring enzymes usually cannot survive the long process times and elevated temperatures used in industry. We are engineering enzymes to be thermostable, to tolerate organic solvents and to use alternative cofactors so that they can be employed as designer biocatalysts for the pharmaceutical and other chemical industries.

Research Impacts

Our research is leading to the development of more sustainable, environmentally friendly, chemical processes to accelerate drug development and improve the safety of medicines. Our studies into the evolution of catalytic promiscuity in P450s reveal how organisms have evolved to deal with chemicals in the environment and provide insights as to how enzymes develop novel functions. More broadly, the methods that we have developed with colleagues at UQ and in industry for the ancestral reconstruction of P450s and their implementation as sophisticated biocatalysts in industry can be applied to the optimisation of other proteins and enzymes for biotechnological application.

Qualifications

  • Doctor of Philosophy, University of Oxford
  • Bachelor (Honours) of Science (Advanced), The University of Queensland

Publications

View all Publications

Grants

View all Grants

Supervision

  • Development of Cytochrome P450 Enzymes as Biocatalysts for Metabolite and Novel Drug Candidate Synthesis for the Pharmaceutical Industry.

    Doctor Philosophy

  • Solar-powered biocatalysis: Using Photosynthesis to Power Fine Chemical Production

    Doctor Philosophy

  • Ancestral reconstruction and characterisation of the CYP2U subfamily

    (2022) Doctor Philosophy

View all Supervision

Available Projects

  • Engineering enzymes for bioremediation of microplastics

    Plastics such as polyethylene (PE) are major pollutants in both terrestrial and aquatic environments because they are not easily degraded in nature. Physico-chemical methods for PE remediation are energy intensive and not economically sustainable, raising the possibility of bioremediation instead. The larvae of the greater wax moth (GWM, Galleria mellonella) feed on beeswax, which is rich in long-chain alkanes, and have recently been shown to consume chemically similar low-density PE at considerably higher rates than those currently reported for PE-degrading microbes. Recent work suggests that P450 enzymes may be involved but the mechanism by which this occurs is not yet clear and there is no consensus on how the degradation is achieved biochemically, or even whether it is carried out entirely by the caterpillars themselves or with a contribution from the gut microbiota. Intriguingly, PE breakdown appears to involve a shift to high pH in the lumen of the insect gut, suggesting these enzymes may operate extracellularly and under very alkaline conditions, both of which are highly unusual for P450 enzymes. This project will involve expressing these enzymes and analysing their activity under the high pH and low oxygen conditions of the gut environment. We will then engineer them by ancestral sequence reconstruction (ASR) to identify thermostable and more pH-neutral forms of the PE-degrading P450s to develop a system in which these enzymes can be used for breakdown of microplastics in wastes.

  • How did koalas evolve to exist entirely on eucalyptus leaves, which are toxic to most mammals?

    The diet of koalas is unique in comprising effectively 100% eucalyptus leaves, which contain a variety of toxic terpenes. Despite the interest in koala conservation and many years of study, we still do not understand how koalas can exist on such a this toxic diet. However a clue has come in the sequencing of the koala genome: compared to other marsupials and mammals more generally, koalas show a dramatic expansion in the CYP2C subfamily of cytochrome P450 enzymes. P450s are regarded as responsible for the metabolism of dietary and other environmental xenobiotics, so we hypothesise that the CYP2C forms in koalas have expanded to deal with the terpenes present in their diet and can oxidise these chemicals to facilitate their clearance from the koala’s circulation.

    This project will test this hypothesis by synthesising the CYP2C enzymes from koalas then expressing them in E. coli with the extant reductase accessory enzyme. We will determine how well the recombinant enzymes metabolise cineole and other eucalyptus terpenes. In so doing, we hope to answer a fundamental question about the biology of this iconic Australian animal, and one that has implications for koala conservation.

    If the hypothesis is proven to be correct (i.e. the extant koala CYP2C forms metabolise terpenes), selected ancestors of these CYP2C enzymes will be inferred, reconstructed and expressed to determine how the ability to metabolise eucalyptus terpenes arose during koala evolution, a model of how proteins evolve new functions.

  • Engineering a sustainable source of strigolactone hormones to improve food security across the world.

    Strigolactones (SLs) are a class of plant hormones that control many traits important for agriculture including shoot and root architecture, nutrient uptake and responses to parasitic weeds. Parasitic weeds stimulated by plant-derived SLs are widespread in arable lands of many developing countries and have devastating impacts on food production. Application of synthetic SLs to infested soils would provide a way to clear arable land of parasitic weeds and greatly enhance food security in the third world. Biotechnological sources of natural or chemically modified SLs would also improve agricultural crop yield and reduce manual labour costs in horticultural industries. The overall objective of this project is to develop means for SL production in biofactories and to improve the potency of synthetic and/or biofactory/engineered SLs. We will do so by analysing the evolution of naturally occurring SL-synthesising enzymes and leveraging ancestral sequence reconstruction to engineer robust novel 'designer' enzymes with specific desired activities.

View all Available Projects

Publications

Book

  • Directed Evolution Library Creation: methods and protocols

    Elizabeth M.J. Gillam, Janine N. Copp and David F. Ackerley eds. (2014). Directed Evolution Library Creation: methods and protocols. 2nd ed. Methods in Molecular Biology, New York, NY United States: Springer. doi: 10.1007/978-1-4939-1053-3

Book Chapter

  • Use of engineered cytochromes P450 for accelerating drug discovery and development

    Thomson, Raine E.S., D'Cunha, Stephlina A., Hayes, Martin A. and Gillam, Elizabeth M.J. (2022). Use of engineered cytochromes P450 for accelerating drug discovery and development. Pharmacology and toxicology of cytochrome P450 – 60th anniversary. (pp. 195-252) edited by Hiroshi Yamazaki. Cambridge, MA, United States: Academic Press. doi: 10.1016/bs.apha.2022.06.001

  • Using the evolutionary history of proteins to engineer insertion-deletion mutants from robust, ancestral templates using Graphical Representation of Ancestral Sequence Predictions (GRASP)

    Ross, Connie M., Foley, Gabriel, Boden, Mikael and Gillam, Elizabeth M. J. (2022). Using the evolutionary history of proteins to engineer insertion-deletion mutants from robust, ancestral templates using Graphical Representation of Ancestral Sequence Predictions (GRASP). Enzyme engineering. (pp. 85-110) edited by Francesca Magnani, Chiara Marabelli and Francesca Paradisi. New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-1826-4_6

  • Directed evolution of enzymes

    Jackson, Colin J., Gillam, Elizabeth M.J. and Ollis, David L. (2020). Directed evolution of enzymes. Comprehensive Natural Products III: Chemistry and biology. (pp. 654-673) London, United Kingdom: Elsevier. doi: 10.1016/B978-008045382-8.00675-4

  • 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

  • Preface

    Gillam, Elizabeth M. J., Copp, Janine N. and Ackerley, David F. (2014). Preface. Directed evolution library creation: methods and protocols. (pp. v-vi) edited by Elizabeth M.J. Gillam, Janine N. Copp and David Ackerley. New York, NY United States: Humana Press.

  • DNA shuffling of cytochrome P450 enzymes

    Behrendorff, James B. Y. H., Johnston, Wayne A. and Gillam, Elizabeth M. J. (2013). DNA shuffling of cytochrome P450 enzymes. Cytochrome P450 protocols. (pp. 177-188) edited by Ian R. Phillips, Elizabeth A. Shepherd and Paul R. Ortiz de Montellano. New York, NY, United States: Humana Press. doi: 10.1007/978-1-62703-321-3_16

  • Measurement of P450 difference spectra using intact cells

    Johnston, Wayne A. and Gillam, Elizabeth M. J. (2013). Measurement of P450 difference spectra using intact cells. Cytochrome P450 protocols. (pp. 189-204) edited by Ian R. Phillips, Elizabeth A. Shepherd and Paul R. Ortiz de Montellano. New York, NY, United States: Humana Press. doi: 10.1007/978-1-62703-321-3_17

  • Directed evolution of enzymes

    Jackson, Colin J., Gillam, Elizabeth M. J. and Ollis, David L. (2010). Directed evolution of enzymes. Comprehensive natural products II chemistry and biology. (pp. 723-749) edited by Lewis Mander and Hung-Wen Liu. Oxford, England, Unied Kingdom: Elsevier.

  • Chemical Defence and Exploitation: Biotransformation of Xenobiotics by Cytochrome P450 Enzymes

    Gillam, E. M. J. and Hunter, D. J. B. (2007). Chemical Defence and Exploitation: Biotransformation of Xenobiotics by Cytochrome P450 Enzymes. Metal Ions in Life Sciences. (pp. 477-560) edited by Astrid Sigel, Helmut Sigel and Roland K. O. Sigel. West Sussex: John Wiley and sons. doi: 10.1002/9780470028155.ch15

Journal Article

Conference Publication

Other Outputs

Grants (Administered at UQ)

PhD and MPhil Supervision

Current Supervision

  • Development of Cytochrome P450 Enzymes as Biocatalysts for Metabolite and Novel Drug Candidate Synthesis for the Pharmaceutical Industry.

    Doctor Philosophy — Principal Advisor

  • Solar-powered biocatalysis: Using Photosynthesis to Power Fine Chemical Production

    Doctor Philosophy — Principal Advisor

    Other advisors:

  • Nano-bioreactors for sustainable biopolymer production

    Doctor Philosophy — Principal Advisor

  • Evolution of cytochrome P450 enzymes in response to dietary and environmental chemicals

    Doctor Philosophy — Principal Advisor

    Other advisors:

  • Nano-scale bioreactors: Protein cages as reusable scaffolds for designer enzymes

    Doctor Philosophy — Principal Advisor

Completed Supervision

Possible Research Projects

Note for students: The possible research projects listed on this page may not be comprehensive or up to date. Always feel free to contact the staff for more information, and also with your own research ideas.

  • Engineering enzymes for bioremediation of microplastics

    Plastics such as polyethylene (PE) are major pollutants in both terrestrial and aquatic environments because they are not easily degraded in nature. Physico-chemical methods for PE remediation are energy intensive and not economically sustainable, raising the possibility of bioremediation instead. The larvae of the greater wax moth (GWM, Galleria mellonella) feed on beeswax, which is rich in long-chain alkanes, and have recently been shown to consume chemically similar low-density PE at considerably higher rates than those currently reported for PE-degrading microbes. Recent work suggests that P450 enzymes may be involved but the mechanism by which this occurs is not yet clear and there is no consensus on how the degradation is achieved biochemically, or even whether it is carried out entirely by the caterpillars themselves or with a contribution from the gut microbiota. Intriguingly, PE breakdown appears to involve a shift to high pH in the lumen of the insect gut, suggesting these enzymes may operate extracellularly and under very alkaline conditions, both of which are highly unusual for P450 enzymes. This project will involve expressing these enzymes and analysing their activity under the high pH and low oxygen conditions of the gut environment. We will then engineer them by ancestral sequence reconstruction (ASR) to identify thermostable and more pH-neutral forms of the PE-degrading P450s to develop a system in which these enzymes can be used for breakdown of microplastics in wastes.

  • How did koalas evolve to exist entirely on eucalyptus leaves, which are toxic to most mammals?

    The diet of koalas is unique in comprising effectively 100% eucalyptus leaves, which contain a variety of toxic terpenes. Despite the interest in koala conservation and many years of study, we still do not understand how koalas can exist on such a this toxic diet. However a clue has come in the sequencing of the koala genome: compared to other marsupials and mammals more generally, koalas show a dramatic expansion in the CYP2C subfamily of cytochrome P450 enzymes. P450s are regarded as responsible for the metabolism of dietary and other environmental xenobiotics, so we hypothesise that the CYP2C forms in koalas have expanded to deal with the terpenes present in their diet and can oxidise these chemicals to facilitate their clearance from the koala’s circulation.

    This project will test this hypothesis by synthesising the CYP2C enzymes from koalas then expressing them in E. coli with the extant reductase accessory enzyme. We will determine how well the recombinant enzymes metabolise cineole and other eucalyptus terpenes. In so doing, we hope to answer a fundamental question about the biology of this iconic Australian animal, and one that has implications for koala conservation.

    If the hypothesis is proven to be correct (i.e. the extant koala CYP2C forms metabolise terpenes), selected ancestors of these CYP2C enzymes will be inferred, reconstructed and expressed to determine how the ability to metabolise eucalyptus terpenes arose during koala evolution, a model of how proteins evolve new functions.

  • Engineering a sustainable source of strigolactone hormones to improve food security across the world.

    Strigolactones (SLs) are a class of plant hormones that control many traits important for agriculture including shoot and root architecture, nutrient uptake and responses to parasitic weeds. Parasitic weeds stimulated by plant-derived SLs are widespread in arable lands of many developing countries and have devastating impacts on food production. Application of synthetic SLs to infested soils would provide a way to clear arable land of parasitic weeds and greatly enhance food security in the third world. Biotechnological sources of natural or chemically modified SLs would also improve agricultural crop yield and reduce manual labour costs in horticultural industries. The overall objective of this project is to develop means for SL production in biofactories and to improve the potency of synthetic and/or biofactory/engineered SLs. We will do so by analysing the evolution of naturally occurring SL-synthesising enzymes and leveraging ancestral sequence reconstruction to engineer robust novel 'designer' enzymes with specific desired activities.

  • Crystallisation of thermostable ancestral cytochrome P450 enzymes

    We have developed ancestral P450 enzymes that are extremely thermostable compared to modern enzymes, making them potentially very useful in industry, since they can withstand long incubations at elevated temperatures. They can be used as ‘off the shelf’ reagents to catalyse useful chemistry, such as in in drug discovery and development, fine chemicals synthesis, and cleaning up the environment. Working with drug companies, we are exploring how they can be best deployed in chemical processes and what structural features make them efficient, robust and specialized. Key to this is obtaining crystal structures of the enzymes to determine why they are more stable.

    We have already obtained crystals of a number of different thermostable P450s so this project would allow a student to make accelerated progress towards the goal of obtaining a structure for high impact publications that would be of great interest to industry as well as the field of protein structural biology and engineering.

  • Scaling up cytochrome P450-mediated biocatalysis for industry

    We have developed ancestral P450 enzymes that can be used as ‘off the shelf’ reagents to catalyse useful chemistry, such as in in drug discovery and development, fine chemicals synthesis, and cleaning up the environment. Working with drug companies, we are exploring how they can be best deployed in chemical processes. This synthetic biology project is part of a collaboration with the Danish Technocal University and the multinational drug company, AstraZeneca, to further engineer these enzymes to be stable to oxidising conditions that currently limit reaction scale-up. It would suit students with a biochemistry, molecular biology or biochemical/process engineering background. A competitive UQ-DTU scholarship is currently open to support this project which would involve the succesful student spending some time in Copenhagen.

  • Synthetic biology of P450s for clean, green, solar-powered chemistry in drug development, bioremediation and biosensors

    We have developed ancestral P450 enzymes that can be used as ‘off the shelf’ reagents to catalyse useful chemistry, such as in in drug discovery and development, fine chemicals synthesis, and cleaning up the environment. Working with drug companies, we are exploring how such biocatalytic processes can be made cheaper and more sustainable. In particular, we can replace the requirement for an expensive redox cofactor (NADPH) by linking the P450s to photosynthesis, to power P450 reactions for clean, green biocatalysis in microalgae.

    This synthetic biology project would suit a student with a biochemistry, molecular biology, plant biology or biochemical engineering background and will be undertaken in collaboration with the pharmaceutical company, AstraZeneca.

This staff member is a UQ Expert for media in the following fields:

Biocatalysis, Enzymes, Drug discovery, Bioremediation, Chemical industries, Drug metabolism, Molecular toxicology, Bacterial expression, Human cytochrome P450 enzymes, P450 enzymes

They are happy to lend their expertise to your articles or broadcasts and share their research discoveries and insights with the community via media channels.

For additional assistance with story ideas, general advice and information or help with seeking further experts, please email the UQ Media Team or telephone (07) 3365 1120.

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ResearcherID: D-1011-2016

ORCID: 0000-0003-0378-793X

Scopus ID: 7003380719

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