Dr Claudia Vickers

Accelerate Mid Career Fellow

Australian Institute for Bioengineering and Nanotechnology

Affiliated Lecturer

School of Chemistry and Molecular Biosciences
Faculty of Science
c.vickers@uq.edu.au
+61 7 334 63958
0405340350

Overview

Dr Vickers works in the fields of isoprenoid biology/metabolic regulation/engineering, carbohydrate metabolism/engineering, and beer systems biology. These diverse areas are linked though understanding fundamental biology and applying this understanding to industrial bioprocesses. In particular, she has an interest in using biology to replace current industrial practices (largely based on finite petrochemical resources) with sustainable, environmentally friendly approaches. To this end, she uses the tools of systems and synthetic biology for metabolic engineering of microbes. Dr Vickers has made seminal contributions to: understanding the role of isoprenoids in plant biochemistry/physiology; elucidating the genetic, molecular and biochemical control isoprene emission; and understanding/engineering sucrose utilization in industrial microbes. She has also developed many enabling tools for molecular biology/synthetic biology in both plants and microbes (transformation vectors, expression control systems, chromosomal integration systems, reporter systems, etc.). Dr Vickers has research programs and student research projects available in the following areas: • Isoprenoid Pathway Engineering • Isoprenoid Biofuels and Industrial Biochemicals • Tools for Synthetic Biology • Synthetic Biology Circuit Construction • Beer Systems Biology • Feedstock Pathway Engineering Dr Vickers is very active in science education, outreach and career advice for early career scientists. She has been invited to act as an advisor on synthetic biology (as an emerging technology) for both the Australian Federal Government and the Institute on Science for Global Policy (an American-based organisation).

Research Interests

  • Isoprenoid Pathway Engineering
    Isoprenoids are a very large class of natural products. Their chemical and structural diversity lends them to a wide variety of industrial applications (e.g. as pharmaceuticals, fuels, rubbers, nutraceuticals, agricultural chemicals, flavours, fragrances, colorants, etc.). They are produced in living cells by two distinct metabolic pathways: the well-known mevalonate (MVA) pathway, which is responsible for production of sterols and related compounds, and the recently-discovered methylerythritol phosphate (MEP) pathway. We are using synthetic biology engineering approaches to improve carbon flux through both of these pathways for production of industrially-useful isoprenoids. The aim of this program is to increase conversion of bioprocess feedstocks (such as sucrose) into the desired end product by whole cell biocatalysts. We have reconstructed synthetic pathways with improved flux in both yeast and E. coli. We are also examining approaches to minimise carbon loss to competing pathways, redirect carbon into the pathways, and scavenge carbon lost to nonspecific reactions.
  • Isoprenoid Biofuels and Industrial Biochemicals
    We are interested in a large variety of industrially-useful isoprenoids. Examples include isoprene, a C5 hydrocarbon that can be polymerised to make synthetic rubber, various C10 (monoterpene) and C15 (sesquiterpene) hydrocarbons that can be used to produce bio-jet fuel/bio-diesel (and in other applications), and isoprenoid plant hormones (such as strigolactones) for agricultural applications. Production of these compounds is non-trivial, since they are not naturally made by E. coli and yeast. In particular, the C10 precursor is typically not available, and must be engineered. Of course, availability of sufficient precursors for bulk production requires substantial engineering of upstream pathways (see above).
  • Tools for Synthetic Biology
    We have developed a variety of synthetic biology tools to facilitate metabolic engineering in both yeast and E. coli. Examples include our expression and integration vectors. The pCEV vectors allow over-expression of multiple genes in yeast using antibiotic resistance for selection. This is particularly useful for industrial strains that do not have engineered auxotrophies, or for heavily engineered strains that have no auxotrophic markers remaining for selection. We also have a vector series for rapid, efficient integration of very large DNA sequences onto the E. coli genome. These plasmids are particularly useful for introduction of multiple genes, for example when reconstructing long metabolic pathways.
  • Synthetic Biology Circuit Construction
    Regulating gene expression at appropriate times during cultivation is very important to help avoid/mitigate problems of metabolic burden (excessive competition between production of the biochemical of interest and core metabolism required for cell growth) and/or product toxicity. We have developed synthetic biology circuits to help control appropriate expression patterns. The native yeast system, naturally used to detect cell density (‘quorum sensing’) was hi-jacked to interface with signal amplification and regulation systems, so that sharp switch-like control of gene expression is achieve in response to increased cell density. This technology is now being applied to a variety of problems.
  • Beer Systems Biology
    Humankind has been brewing beer - or what could reasonably pass as beer - for at least 11,000 years. We know a great deal about the bioprocess requirements for beer brewing, but we know much less about the biology. Beer brewing requires three different living organisms: barley, hops, and yeast. We are using systems biology to investigate the interactions between these three different organisms throughout the brewing process. These interactions are critical for a number of different beer quality trains, including foam quality, staling, flavours and aromas.
  • Feedstock Pathway Engineering
    For production of bulk biochemicals using microbes, the carbon source is the key cost driver. Sucrose from sugarcane is preferable to corn-derived glucose as a carbon source because (1) it is highly abundant (2) sugarcane has a very high energy yield per hectare compared to corn (3) sugar is not a staple food crop, and (4) waste biomass can be used to produce electricity, making processes cheaper and more carbon-friendly. Sucrose is a major agricultural product in Australia. However, most industrial strains of E. coli cannot utilise it as a carbon source. To better understand sucrose utilisation, we sequenced the genome of a sucrose-utilising E. coli strain and generated an in silico genome-scale metabolic model. We then developed methods to improve sucrose utilisation in this strain, and to reproducibly engineer efficient sucrose utilisation in industrial E. coli strains. Engineered strains producing polyhydroxybutyrate (a polymer that can be used to make biodegradeable plastics) and peptide bio-surfactants make as much or more bio-product when growing on sucrose than on glucose.

Qualifications

  • Doctor of Philosophy, The University of Queensland
  • BSc (Hons), The University of Queensland

Publications

View all Publications

Supervision

View all Supervision

Available Projects

  • I have two positions available for high quality PhD candidates to work in the area of isoprenoid pathway metabolic regulation/pathway engineering. Prospective students will be supported to apply for UQ PhD scholarships, and will need to have a strong CV to be competitive. Email me a copy of your CV if you are interested and we can discuss further.

View all Available Projects

Publications

Book Chapter

  • Vickers, Claudia E., Behrendorff, James B. Y. H., Bongers, Mareike, Brennan, Timothy C. R., Bruschi, Michele and Nielsen, Lars K. (2015). Production of industrially-relevant isoprenoid compounds in engineered microbes. In Birgit Kamm (Ed.), Microorganisms in biorefineries (pp. 303-334) Berlin, Heidelberg: Springer. doi:10.1007/978-3-662-45209-7_11

Journal Article

Conference Publication

  • Vickers, Claudia E., Sabri, Suriana, Bongers, Mareike and Nielsen, Lars (2013). Understanding metabolic control of carbon flux through the MEP pathway: a systems and synthetic biology approach. In: 11th International Meeting on Biosynthesis, Function and Biotechnology of Isoprenoids in Terrestrial and Marine Organisms: TERPNET 2013. Book of Abstracts. TERPNET 2013: 11th International Meeting on Biosynthesis, Function and Biotechnology of Isoprenoids in Terrestrial and Marine Organisms, Kolymvari, Crete, Greece, (250-250). 1-5 June, 2013.

  • Hartley, M. and Vickers, C. E. (2012). Improving risk analysis through globally harmonized. In: World Congress on Risk 2012: Final Program. World Congress on Risk 2012, Sydney, Australia, (41-41). 17-20 July 2012.

  • Vickers, C. E. (2012). Metabolic engineering using systems and synthetic biology. In: World Congress on Risk 2012: Final Program. World Congress on Risk 2012, Sydney, Australia, (75-75). 17-20 July 2012.

  • Vickers, Claudia E., Archer, Colin, Bruschi, Michele, Arifin, Yalun, Sabri, Suriana, Boyes, Simon and Nielsen, Lars K. (2011). Sucrose-to-bioproducts: Engineering a sucrose-based E. coli platform for industrial bioproduction. In: ICBE 2011: International Conference on Biomolecular Engineering, San Francisco, CA, U.S.A., (). 16-19 January 2011.

  • Bruschi, Michele, Boyes, Simon, Vickers, Claudia E. and Niel, Lars (2010). Development of a transferable sucrose utilization cassette for industrial relevant E. coli. In: 14th International Biotechnology Symposium and Exhibition (IBS-2008), Rimini, Italy, (S549-S549). 14-18 September 2010. doi:10.1016/j.jbiotec.2010.09.912

  • Arifin, Y., Sugiarto, H., Sabri, S., Kromer, J. O., Vickers, C. E. and Nielsen, L. K. (2010). Metabolic engineering of sucrose utilizing Escherichia coli for polyhydroxybutyrate production. In: 14th International Biotechnology Symposium and Exhibition (IBS-2008), Rimini, Italy, (S72-S73). 14-18 September 2010. doi:10.1016/j.jbiotec.2010.08.189

  • Archer, C.T., Arifin, Y., Nielsen, L.K, Sugiarto, A. and Vickers, C.E. (2010). Sucrose-to-BioProducts: Metabolic engineering for PHB in sucrose-utilising E. coli. In: 11th International Symposium on Genetics of Industrial Microorganisms GIM, Melbourne, Australia, (). 28 June – 1 July 2010.

  • Vickers, Claudia E., Bruschi, M., Boyes, S. J. and Nielsen, L.K. (2010). Transferrable sucrose utilization in E. coli. In: Metabolic Engineering VIII: Metabolic Engineering for Green Growth, Jeju Island, Korea, (). 13-17 June 2010.

  • Vickers, C. E., Gershenzon, J., Lerdau, M. T. and Loreto, F. (2009). A unified mechanism of action for volatile isoprenoids in plant abiotic stress. In: TERPNET 2009. 9th International Meeting: Biosynthesis and Function of Isoprenoids in Plants, Microorganisms and Parasites, Tokyo, Japan, (). 25-29 May 2009.

  • Cojocariu, C., Vickers, C., Velikova, V., Hewitt, N. and Mullineaux, P. (2007). Isoprene-induced protection in tobacco plants exposed to elevated ozone concentration. In: Comparative Biochemistry and Physiology. A, Molecular & Integrative Physiology. Proceedings of: Russell V. Baudinette Memorial Symposium. Annual Main Meeting of the Society for Experimental Biology, Glasgow, Scotland, (263-264). 31 March - 4 April, 2007. doi:10.1016/j.cbpa.2007.01.668

  • Cojocariu, C., Hewitt, N., Vickers, C., Mullineaux, P. and Velikova, V. (2007). Isoprene-induced protection in tobacco plants exposed to elevated ozone concentration. In: Annual Main Meeting of the Society for Experimental Biology, Glasgow, Scotland, (S263-S264). 31 March - 4 April 2007. doi:10.1016/j.cbpa.2007.01.668

  • Vickers, C. E., Possell, M., Cojocariu, C., Velikova, V., Laothawornkitkul, J., Mullineaux, P. M. and Hewitt, C. N. (2007). Molecular biology of isoprene emission in poplar and transgenic tobacco. In: Gordon Research Conference on Biogenic Volatiles and the Atmosphere. Gordon Research Conference on Biogenic Volatiles and the Atmosphere, Ventura, California, U.S.A, (). 25 Feb - 2 Mar, 2007.

  • Vickers, C.E., Possell, M., Cojocariu, C., Velikova, V., Laothawornkitkul, J., Mullineaux, P.M. and Hewitt, C.N. (2007). Molecular characterisation of isoprene synthase in poplar and transgenic tobacco. In: 8th International Meeting: Biosynthesis and Function of Isoprenoids in Plants, Microorganisms and Parasites. TERPNET 2007, Strasbourg, France, (). 30 Apr - 4 May, 2007.

  • Vickers, C. E., Possell, E., Hewitt, C. N. and Mullineaux, P. M. (2006). Molecular biology of isoprene emission in poplar and transgenic tobacco. In: Plastid Preview 2006, Essex University, Colchester, (). 11-12 September, 2006.

  • Gresshoff, P. M., Carroll, B. J., Gualtieri Gonzalez, G. S., Vickers, C., Kuen, P., Huang, C., Scott, P. T., Kinkema, M. D., Men, A., Stiller, J., Jiang, Q., Laniya, T.S., Buzas, D. M., Miyahara, A., Indrasumunar, A., Nontachaiyapoom, S., Hoffmann, D., Biswas, B., Wells, T. J., So, H., Pregelj, L. and Dong, X. (2004). Functional genomic analysis of nodule development in soybean and Lotus Japonicus. In: ComBio 2004. Com Bio 2004, Intercontinental Burswood Resort, Perth, Australia, (36-36). 26-30 September, 2004.

  • Vickers, C.E., Gresshoff, P.M. and Xue, G-P. (2003). An oat globulin promoter drives endosperm-specific expression in transgenic barley. In: Proceedings of the 7th International Congress of Plant Molecular Biology. ISPMB, 2003, Barcelona, Spain, (). 23-28 June, 2003.

  • Gresshoff, P.M., Vickers, C. E. and Xue, G.P. (2001). Deletion analysis of an endosperm-specific promoter isolated from oat. In: Combined Conference Abstracts: ComBio 2001. ComBio2001: A New Dimension, Canberra, ACT, Australia, (Pos-1-143-Pos-1-143). 1-4 October 2001.

  • Vickers, C., Gresshoff, P. M. and Xue, G. (2000). Activity of seed storage proteins and barley and wheat. In: 15th Australiasian Biotechnology Conference. ABA 2000 Biotechnology: our passport to the next millenium, Brisbane, (60). 2-6 July, 2000.

  • Vickers, C., Gresshoff, P. M. and Xue, G. (2000). Analysis of Endosperm-specific promoters in cereal crops. In: Combined Conference Abstracts: 44th Annual ASBMB, 40th Annual ASPP, Annual NZSBMB, 22nd Annual NZSPP. Com Bio 2000, Wellington, NZ, (Poster2-101). 11-14 Dec, 2000.

  • Vickers, C., Gresshoff, P. M. and Xue, G. (2000). Promoting agro-revolution in the cereal world. In: 15th Australasian Biotechnology Conference. ABA 2000 Biotechnology: Our Passport to the Next Millenium, Brisbane, (60). 2-6 July, 2000.

Other Outputs

Grants (Administered at UQ)

PhD and MPhil Supervision

Current Supervision

  • Doctor Philosophy — Principal Advisor

    Other advisors:

  • Doctor Philosophy — Associate Advisor

  • 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.

  • I have two positions available for high quality PhD candidates to work in the area of isoprenoid pathway metabolic regulation/pathway engineering. Prospective students will be supported to apply for UQ PhD scholarships, and will need to have a strong CV to be competitive. Email me a copy of your CV if you are interested and we can discuss further.