Dr Ellis O’Neill

Research interests

Biomolecular engineering of microbes for natural product discovery and production.

 

My research is focussed on developing and applying synthetic biology approaches to the Euglenozoa, a monophylletic group including both free living algae and parasitic eukaryotes. I am taking a multidisciplinary approach to establish metabolic capacity and utility of different species in this group. This includes developing transformation protocols, characterising metabolic capacity and applying high-throughput sequencing approaches for novel pathway discovery. These disparate approaches are used to facilitate targeted engineering of complex metabolic pathways for the production of compounds for industrial, biotechnology and medicinal applications.

Contact details

ellis.oneill@plants.ox.ac.uk

+44 (0)1865 275024

Publications

Kelly, S., Ivens, A., Mott,G. A., O’Neill, E. C., Emms, D., Macleod, O., Voorheis, P., Tyler, K., Clark, M., Matthews, J., Matthews, K.,  Carrington, M. C. An Alternative Strategy for Trypanosome Survival in the Mammalian Bloodstream Revealed through Genome and Transcriptome Analysis of the Ubiquitous Bovine Parasite Trypanosoma (Megatrypanum) theileriGenome Biology and Evolution (2017) 9, 2093-2109 DOI: 10.1093/gbe/evx152

O’Neill, E. C., Pergolizzi, G., Stevenson, C. E. M., Lawson, D. M., Nepogodiev, S. A., and Field, R. A. Cellodextrin phosphorylase from Clostridium thermocellum: X-ray crystal structure and substrate specificity analysis. Carbohydrate Research (2017) DOI: 10.1016/j.carres.2017.07.005

O’Neill, E. C. and Kelly, S. Engineering biosynthesis of high-value compounds in photosynthetic organisms. Critical Reviews in Biotechnology (2017) 37, 779-802 DOI: 10.1080/07388551.2016.1237467

O’Neill, E. C. Biomolecular engineering of micro-organisms for natural products production. In: Reedijk, J. (Ed.) Reference Module in Chemistry, Molecular Sciences and Chemical Engineering. Waltham, MA: Elsevier. 22-Apr-2017 doi:10.1016/B978-0-12-409547-2.12791-X

Crüsemann, M., O’Neill, E. C., Larson, C. B., Melnik, A. V., Floros, D. J., da Silva, R. R., Jensen, P. R, Dorrestein, B. C., and Moore, B. S. Prioritizing natural product diversity in a collection of 146 bacterial strains based on growth and extraction protocols. Journal of Natural Products (2017) 80, 588-597 DOI:10.1021/acs.jnatprod.6b00722

Ivanova, I. M., Nepogodiev, S.A., Saalbach, G., O'Neill, E. C., Urbaniak, M. D., Ferguson, M. A. J., Gurcha, S. S., Besra, G. S., Field R. A. Fluorescent mannosides serve as acceptor substrates for glycosyltransferase and sugar-1-phosphate transferase activities in Euglena gracilis membranes. Carbohydrate Research (2017) 438, 26-38 DOI: 10.1016/j.carres.2016.11.017

Wang, M., Carver, J., Phelan, V., Sanchez, L., Garg, N., Peng, Y., Nguyen, D., Watrous, J., Kapono, C., Luzzatto-Knaan, T., Porto, C., Bouslimani, A., Melnik, A., Meehan, M., Liu, W.-T., Cruesemann, M., Boudreau, P., Esquenazi, E., Sandoval-Calderón, M., Kersten, R., Pace, L., Quinn, R., Duncan, K., Hsu, C.-C., Floros, D., Gavilan, R., kleigrewe, K., Northen, T., Dutton, R., Parrot, D., Carlson, E., Aigle, B., Michelsen, C., Jelsbak, L., Sohlenkamp, C., Pevzner, P., Edlund, A., McLean, J., Piel, J., Murphy, B., Gerwick, L., Liaw, C.-C., Yang, Y.-L., Humpf, H.-U., Mansson, M., Keyzers, R., Sims, A., Johnson, A., Sidebottom, A., Sedio, B., Klitgaard, A., Larson, C., P, C. B., Torres-Mendoza, D., Gonzalez, D., Silva, D., Marques, L., Demarque, D., Pociute, E., O'Neill, EC., Briand, E., Helfrich, E., Granatosky, E., Glukhov, E., Ryffel, F., Houson, H., Mohimani, H., Kharbush, J., Zeng, J., Vorholt, J., Kurita, K., Charusanti, P., McPhail, K., Nielsen, K., Vuong, L., Elfeki, M., Traxler, M., Engene, N., Koyama, N., Vining, O., Baric, R., Silva, R., Mascuch, S., Tomasi, S., Jenkins, S., Macherla, V., Hoffman, T., Agarwal, V., Williams, P., Dai, J., Neupane, R., Gurr, J., Rodríguez, A., Lamsa, A., Zhang, C., Dorrestein, K., Duggan, B., Almaliti, J., Allard, P.-M., Phapale, P., Nothias, L.-F., Alexandrov, T., Litaudon, M., Wolfender, J.-L., Kyle, J., Metz, T., Peryea, T., Nguyen, D.-T., Leer, D. V., Shinn, P., Jadhav, A., Mueller, R., Waters, K., Shi, W., Liu, X., Zhang, L., Knight, R., Jensen, P., Palsson, B., Pogliano, K., Linington, R., Gutiérrez, M., Lopes, N., Gerwick, W., Moore, B., and Dorrestein, P. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology (2016) 34, 828-837 DOI: 10.1038/nbt.3597

O'Neill, E. C., Saalbach, G., and Field, R. A. Gene discovery for synthetic biology: exploring the novel natural product biosynthetic capacity of eukaryotic microalgae. Methods in Enzymology (2016) 576, 99-120 DOI: 10.1016/bs.mie.2016.03.005

O’Neill, E. C., Stevenson, C. E. M., Tantanarat, K., Latousakis, D., Donaldson, M.I., Rejzek, M., Nepogodiev, S. A., Limpaseni, T., Field, R. A. and Lawson, D. M. Structural dissection of the maltodextrin disproportionation cycle of the Arabidopsis plastidial enzyme DPE1. Journal of Biological Chemistry (2015) 290, 29834 DOI: 10.1074/jbc.M115.682245

O’Neill, E. C., Trick, M., Henrissat, B. and Field, R. A. Euglena in time: Evolution, control of central metabolic processes and multi-domain proteins in carbohydrate and natural product biochemistry. Perspectives in Science (2015) 6, 84-93 DOI:10.1016/j.pisc.2015.07.002

Tang, X., Li, J., Millán-Aguiñaga, N., Zhang, J. J., O’Neill, E. C., Ugalde, J. A., Jensen, P. R., Mantovani, S. M. and Moore, B. S. Identification of thiotetronic acid antibiotic biosynthetic pathways by target-directed genome mining. ACS Chemical Biology (2015) 10, 2841-2849 DOI: 10.1021/acschembio.5b00658

O’Neill, E. C., and Field, R. A. Underpinning starch biology with in vitro studies on carbohydrate-active enzymes and biosynthetic glycomaterialsFrontiers in Bioengineering and Biotechnology (2015) 3, 136 DOI:  10.3389/fbioe.2015.00136

O’Neill, E. C., Trick, M., Hill, L., Rejzek, M., Dusi, R. G., Hamilton, C. J., Zimba, P. V., Henrissat, B. and Field, R. A. The transcriptome of Euglena gracilis reveals unexpected metabolic capabilities for carbohydrate and natural product biochemistry. Molecular Biosystems (2015) 11, 2808-2820 DOI: 10.1039/C5MB00319A

O’Neill, E. C., Stevenson, C. E. M., Paterson, M. J., Rejzek, M., Chauvin, A.-L., Lawson, D. M., and Field, R. A. Crystal structure of a novel two domain GH78 family α-rhamnosidase from Klebsiella oxytoca with rhamnose bound. Proteins: Structure, Function, and Bioinformatics (2015) 83, 1742-1749 DOI: 10.1002/prot.24807

Wagstaff, B. A., Rejzek, M., Pesnot, T., Tedaldi, L. M., Caputi, L., O’Neill, E. C., Benini, S., Wagner, G. K., and Field, R. A. Enzymatic synthesis of nucleobase-modified UDP-sugars: scope and limitations. Carbohydrate Research (2015) 404, 17-25 DOI: 10.1016/j.carres.2014.12.005

O’Neill, E. C., and Field, R. A. Enzymatic synthesis using glycoside phosphorylases. Carbohydrate Research (2015) 403, 23-37 DOI: 10.1016/j.carres.2014.06.010

O'Neill, E. C., Rashid, A. M., Stevenson, C. E. M., Hetru, A.-C., Gunning, A. P., Rejzek, M., Nepogodiev, S. A., Bornemann, S., Lawson, D. M., and Field, R. A. Sugar-coated sensor chip and nanoparticle surfaces for the in vitro enzymatic synthesis of starch-like materials. Chemical Science (2014) 5, 341-350 DOI: 10.1039/C3SC51829A

Tantanarat, K., O’Neill, E. C., Rejzek, M., Field, R. A., and Limpaseni, T. Expression and characterization of 4-α-glucanotransferase genes from Manihot esculenta Crantz and Arabidopsis thaliana and their use for the production of cycloamyloses. Process Biochemistry (2014) 49, 84-89 DOI: 10.1016/j.procbio.2013.10.009

O’Neill, E. C., and Field, R. A. Antibiotics: Blocking bacterial defences. Nature Chemistry (2013) 5, 642-643 DOI: 10.1038/nchem.1718

Caputi, L., Rejzek, M., Louveau, T., O’Neill, E. C., Hill, L., Osbourn, A., and Field, R. A. A one-pot enzymatic approach to the O-fluoroglucoside of N-methylanthranilate. Bioorganic and Medicinal Chemistry (2013) 21, 4762-4767 DOI: 10.1016/j.bmc.2013.05.057

Tantanarat, K., Rejzek, M., O’Neill, E., Ruzanski, C., Hill, L., Fairhurst, S. A., Limpaseni, T., and Field, R. A. An expedient enzymatic route to isomeric 2-, 3- and 6-monodeoxy-monofluoro-maltose derivatives. Carbohydrate Research (2012) 358, 12-18 DOI: 10.1016/j.carres.2012.05.026

 

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